[med-svn] [Git][med-team/cwltool][upstream] 3 commits: New upstream version 1.0.20180923172926
Michael R. Crusoe pushed to branch upstream at Debian Med / cwltool Commits: 6bd1e0df by Michael R. Crusoe at 2018-10-03T11:40:24Z New upstream version 1.0.20180923172926 - - - - - 62074824 by Michael R. Crusoe at 2018-12-07T06:35:37Z New upstream version 1.0.20181201184214 - - - - - 8b0ef4b2 by Michael R. Crusoe at 2018-12-21T13:46:10Z New upstream version 1.0.20181217162649+dfsg - - - - - 15 changed files: - + LICENSE.txt - MANIFEST.in - Makefile - PKG-INFO - README.rst - cwltool.egg-info/PKG-INFO - cwltool.egg-info/SOURCES.txt - cwltool.egg-info/entry_points.txt - cwltool.egg-info/requires.txt - cwltool.py - cwltool/__init__.py - cwltool/__main__.py - cwltool/argparser.py - cwltool/builder.py - + cwltool/checker.py The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/cwltool/compare/9c74d1573d4c43142d065360a0c436f74d341b28...8b0ef4b2d564ca223d97ca0a1dd4f34561f745ee -- View it on GitLab: https://salsa.debian.org/med-team/cwltool/compare/9c74d1573d4c43142d065360a0c436f74d341b28...8b0ef4b2d564ca223d97ca0a1dd4f34561f745ee You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/cwltool][master] 17 commits: New upstream version 1.0.20180923172926
Michael R. Crusoe pushed to branch master at Debian Med / cwltool Commits: 6bd1e0df by Michael R. Crusoe at 2018-10-03T11:40:24Z New upstream version 1.0.20180923172926 - - - - - 62074824 by Michael R. Crusoe at 2018-12-07T06:35:37Z New upstream version 1.0.20181201184214 - - - - - cf2f962b by Michael R. Crusoe at 2018-12-21T13:36:07Z New upstream version 1.0.20180923172926 - - - - - a88e82ec by Michael R. Crusoe at 2018-12-21T13:36:46Z 1.0.20180923172926-1 - - - - - 9818eec2 by Michael R. Crusoe at 2018-12-21T13:36:47Z New upstream version 1.0.20181201184214 - - - - - 3869bf3e by Michael R. Crusoe at 2018-12-21T13:36:47Z 1.0.20181201184214 - - - - - 0e438674 by Michael R. Crusoe at 2018-12-21T13:36:47Z -- - - - - - 00638474 by Michael R. Crusoe at 2018-12-21T13:36:47Z Remove --provenance feature until python3-prov 1.5.2+ issue is resolved. - - - - - b1b8bd89 by Michael R. Crusoe at 2018-12-21T13:36:48Z cleanups - - - - - 64c77488 by Michael R. Crusoe at 2018-12-21T13:45:56Z exclude jshint - - - - - 8b0ef4b2 by Michael R. Crusoe at 2018-12-21T13:46:10Z New upstream version 1.0.20181217162649+dfsg - - - - - fa61ff51 by Michael R. Crusoe at 2018-12-21T13:46:11Z Update upstream source from tag upstream/1.0.20181217162649+dfsg Update to upstream version 1.0.20181217162649+dfsg with Debian dir 323e93fc2835d02fcb1ebc90221800b89ffc8fde - - - - - e6fb633c by Michael R. Crusoe at 2018-12-21T13:46:21Z fix changelog - - - - - db2e18f8 by Michael R. Crusoe at 2018-12-21T13:58:32Z refresh patches - - - - - 716236b2 by Michael R. Crusoe at 2018-12-21T14:18:46Z Fix manpage - - - - - 7d559728 by Michael R. Crusoe at 2018-12-21T14:28:47Z fix spelling, add exec line - - - - - 4c4548b1 by Michael R. Crusoe at 2018-12-21T15:36:04Z cleanup test output - - - - - 15 changed files: - + LICENSE.txt - MANIFEST.in - Makefile - PKG-INFO - README.rst - cwltool.egg-info/PKG-INFO - cwltool.egg-info/SOURCES.txt - cwltool.egg-info/entry_points.txt - cwltool.egg-info/requires.txt - cwltool.py - cwltool/__init__.py - cwltool/__main__.py - cwltool/argparser.py - cwltool/builder.py - + cwltool/checker.py The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/cwltool/compare/82c253c43d3cd8f1e308ecd2163bd921a69e65cc...4c4548b1f950e5a4aa9ff767a45cf1be587ed123 -- View it on GitLab: https://salsa.debian.org/med-team/cwltool/compare/82c253c43d3cd8f1e308ecd2163bd921a69e65cc...4c4548b1f950e5a4aa9ff767a45cf1be587ed123 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/cwltool] Deleted branch py3
Michael R. Crusoe deleted branch py3 at Debian Med / cwltool -- You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/htslib] Pushed new tag debian/1.9-6
Michael R. Crusoe pushed new tag debian/1.9-6 at Debian Med / htslib -- View it on GitLab: https://salsa.debian.org/med-team/htslib/tree/debian/1.9-6 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/htslib][master] Partial Revert "Add libdeflate for DEFLATE based (de)compression and its crc32 implementation."
Michael R. Crusoe pushed to branch master at Debian Med / htslib Commits: 147dd806 by Michael R. Crusoe at 2018-12-06T06:59:28Z Partial Revert Add libdeflate for DEFLATE based (de)compression and its crc32 implementation. This reverts commit bc33ca5af9a047ad3e27022953cccedbfcd912ef. - - - - - 3 changed files: - debian/changelog - debian/control - debian/rules Changes: = debian/changelog = @@ -1,3 +1,10 @@ +htslib (1.9-6) unstable; urgency=medium + + * Revert libdeflate for DEFLATE based (de)compression and its crc32 +implementation. + + -- Michael R. Crusoe Wed, 05 Dec 2018 22:59:23 -0800 + htslib (1.9-5) unstable; urgency=medium * Add libdeflate for DEFLATE based (de)compression and its crc32 = debian/control = @@ -11,8 +11,7 @@ Build-Depends: debhelper (>= 11~), libcurl4-gnutls-dev, liblzma-dev, libssl-dev, - zlib1g-dev, - libdeflate-dev + zlib1g-dev Standards-Version: 4.2.1 Vcs-Browser: https://salsa.debian.org/med-team/htslib Vcs-Git: https://salsa.debian.org/med-team/htslib.git = debian/rules = @@ -20,7 +20,7 @@ override_dh_auto_configure: # create clean copy of test dir cp -a test test_backup autoconf - dh_auto_configure -- --enable-libcurl --enable-gcs --enable-s3 + dh_auto_configure -- --enable-libcurl override_dh_auto_build: dh_auto_build -- \ View it on GitLab: https://salsa.debian.org/med-team/htslib/commit/147dd8065ebf3de7d68827ce34b14c84f5904bad -- View it on GitLab: https://salsa.debian.org/med-team/htslib/commit/147dd8065ebf3de7d68827ce34b14c84f5904bad You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/htslib] Pushed new tag debian/1.9-5
Michael R. Crusoe pushed new tag debian/1.9-5 at Debian Med / htslib -- View it on GitLab: https://salsa.debian.org/med-team/htslib/tree/debian/1.9-5 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/spdlog][pristine-tar] pristine-tar data for spdlog_1.2.1.orig.tar.gz
Michael R. Crusoe pushed to branch pristine-tar at Debian Med / spdlog Commits: 2e34ca1f by Michael R. Crusoe at 2018-11-29T07:54:25Z pristine-tar data for spdlog_1.2.1.orig.tar.gz - - - - - 2 changed files: - + spdlog_1.2.1.orig.tar.gz.delta - + spdlog_1.2.1.orig.tar.gz.id Changes: = spdlog_1.2.1.orig.tar.gz.delta = Binary files /dev/null and b/spdlog_1.2.1.orig.tar.gz.delta differ = spdlog_1.2.1.orig.tar.gz.id = @@ -0,0 +1 @@ +6ebd2571cd4c7d099a2291fa6765c9c92d07f8d6 View it on GitLab: https://salsa.debian.org/med-team/spdlog/commit/2e34ca1fb62c2098c071d21876538676d74b9bc8 -- View it on GitLab: https://salsa.debian.org/med-team/spdlog/commit/2e34ca1fb62c2098c071d21876538676d74b9bc8 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/spdlog] Pushed new tag upstream/1.2.1
Michael R. Crusoe pushed new tag upstream/1.2.1 at Debian Med / spdlog -- View it on GitLab: https://salsa.debian.org/med-team/spdlog/tree/upstream/1.2.1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/htslib][master] 2 commits: Add libdeflate for DEFLATE based (de)compression and its crc32 implementation.
Michael R. Crusoe pushed to branch master at Debian Med / htslib
Commits:
bc33ca5a by Michael R. Crusoe at 2018-12-05T04:46:14Z
Add libdeflate for DEFLATE based (de)compression and its crc32 implementation.
- - - - -
81e1ecba by Michael R. Crusoe at 2018-12-05T04:56:22Z
Re-add mipsel to tabix libhts-dev as well. (Closes: #915404)
- - - - -
3 changed files:
- debian/changelog
- debian/control
- debian/rules
Changes:
=
debian/changelog
=
@@ -1,3 +1,11 @@
+htslib (1.9-5) unstable; urgency=medium
+
+ * Add libdeflate for DEFLATE based (de)compression and its crc32
+implementation.
+ * Re-add mipsel to tabix & libhts-dev as well. (Closes: #915404)
+
+ -- Michael R. Crusoe Tue, 04 Dec 2018 20:56:12
-0800
+
htslib (1.9-4) unstable; urgency=medium
* Add Breaks: python-pysam (<< 0.15~), python3-pysam (<< 0.15~)
=
debian/control
=
@@ -11,7 +11,8 @@ Build-Depends: debhelper (>= 11~),
libcurl4-gnutls-dev,
liblzma-dev,
libssl-dev,
- zlib1g-dev
+ zlib1g-dev,
+ libdeflate-dev
Standards-Version: 4.2.1
Vcs-Browser: https://salsa.debian.org/med-team/htslib
Vcs-Git: https://salsa.debian.org/med-team/htslib.git
@@ -37,7 +38,7 @@ Description: C library for high-throughput sequencing data
formats
new index and then for the old if the new index is absent.
Package: libhts-dev
-Architecture: amd64 arm64 armel armhf mips mips64el ppc64el s390x alpha hppa
ia64 kfreebsd-amd64 m68k powerpc powerpcspe ppc64 riscv64 sh4 sparc64 x32
+Architecture: amd64 arm64 armel armhf mips mips64el mipsel ppc64el s390x alpha
hppa ia64 kfreebsd-amd64 m68k powerpc powerpcspe ppc64 riscv64 sh4 sparc64 x32
Multi-Arch: same
Section: libdevel
Depends: libhts2 (= ${binary:Version}),
@@ -97,7 +98,7 @@ Description: Test data for HTSlib
This package contains test files and scripts for the HTSlib.
Package: tabix
-Architecture: amd64 arm64 armel armhf mips mips64el ppc64el s390x alpha hppa
ia64 kfreebsd-amd64 m68k powerpc powerpcspe ppc64 riscv64 sh4 sparc64 x32
+Architecture: amd64 arm64 armel armhf mips mips64el mipsel ppc64el s390x alpha
hppa ia64 kfreebsd-amd64 m68k powerpc powerpcspe ppc64 riscv64 sh4 sparc64 x32
Depends: ${misc:Depends},
${shlibs:Depends}
Description: generic indexer for TAB-delimited genome position files
=
debian/rules
=
@@ -20,7 +20,7 @@ override_dh_auto_configure:
# create clean copy of test dir
cp -a test test_backup
autoconf
- dh_auto_configure -- --enable-libcurl
+ dh_auto_configure -- --enable-libcurl --enable-gcs --enable-s3
override_dh_auto_build:
dh_auto_build -- \
View it on GitLab:
https://salsa.debian.org/med-team/htslib/compare/47eee749bf3f26002b56a26681ad93a895270d13...81e1ecba421cf8144072fc212f8efa5b97844a0a
--
View it on GitLab:
https://salsa.debian.org/med-team/htslib/compare/47eee749bf3f26002b56a26681ad93a895270d13...81e1ecba421cf8144072fc212f8efa5b97844a0a
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[med-svn] [Git][med-team/spades] Pushed new tag debian/3.13.0+dfsg-2_0jemalloc5
Michael R. Crusoe pushed new tag debian/3.13.0+dfsg-2_0jemalloc5 at Debian Med / spades -- View it on GitLab: https://salsa.debian.org/med-team/spades/tree/debian/3.13.0+dfsg-2_0jemalloc5 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/spades] Pushed new branch experimental
Michael R. Crusoe pushed new branch experimental at Debian Med / spades -- View it on GitLab: https://salsa.debian.org/med-team/spades/tree/experimental You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/spades] Deleted branch experimental
Michael R. Crusoe deleted branch experimental at Debian Med / spades -- You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/gbwt][master] 3 commits: skip tests for now
Michael R. Crusoe pushed to branch master at Debian Med / gbwt
Commits:
aeea3452 by Michael R. Crusoe at 2018-12-14T07:37:14Z
skip tests for now
- - - - -
51f3fca4 by Michael R. Crusoe at 2018-12-14T07:40:59Z
install the static library
- - - - -
7a13f094 by Michael R. Crusoe at 2019-01-10T15:44:27Z
set -DNDEBUG as per upstream
https://github.com/jltsiren/gbwt/issues/2#issuecomment-447283489
- - - - -
3 changed files:
- debian/control
- debian/rules
- debian/tests/control
Changes:
=
debian/control
=
@@ -12,7 +12,7 @@ Homepage: https://github.com/jltsiren/gbwt
Package: libgbwt-dev
Section: libdevel
Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
+Depends: ${misc:Depends}
Description: Substring index for paths in a graph
Graph BWT is an independent implementation of the graph extension (gPBWT) of
the positional Burrows-Wheeler transform (PBWT). Its initial purpose is to
=
debian/rules
=
@@ -15,15 +15,21 @@ include /usr/share/dpkg/default.mk
#specified by
<https://reproducible-builds.org/specs/source-date-epoch/>
# for hardening you might like to uncomment this:
-# export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+CXXFLAGS:=$(shell dpkg-buildflags --get CXXFLAGS) -DNDEBUG
%:
dh $@
override_dh_auto_build:
- dh_auto_build -- MY_CXX=g++ INC_DIR=/usr/include LIB_DIR=/usr/lib
+ dh_auto_build -- CXXFLAGS="$(CXXFLAGS)" MY_CXX=g++ INC_DIR=/usr/include
LIB_DIR=/usr/lib
+
+override_dh_auto_install:
+ dh_auto_install
+ mkdir -p debian/libgbwt-dev/usr/lib/$(shell dpkg-architecture --query
DEB_HOST_MULTIARCH)/
+ cp libgbwt.a debian/libgbwt-dev/usr/lib/$(shell dpkg-architecture
--query DEB_HOST_MULTIARCH)/
override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
- dh_auto_test -- MY_CXX=g++ INC_DIR=/usr/include LIB_DIR=/usr/lib
+ dh_auto_test -- CXXFLAGS="$(CXXFLAGS)" MY_CXX=g++ INC_DIR=/usr/include
LIB_DIR=/usr/lib
endif
=
debian/tests/control
=
@@ -1,3 +1,3 @@
-Tests: run-unit-test
-Depends: @
-Restrictions: allow-stderr
+#Tests: run-unit-test
+#Depends: @
+#Restrictions: allow-stderr
View it on GitLab:
https://salsa.debian.org/med-team/gbwt/compare/25d7af4b0ba43273e22ae5a49efaaf728065b2f1...7a13f09417ec471ab92ade8bd5b714cfa3efeaec
--
View it on GitLab:
https://salsa.debian.org/med-team/gbwt/compare/25d7af4b0ba43273e22ae5a49efaaf728065b2f1...7a13f09417ec471ab92ade8bd5b714cfa3efeaec
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[med-svn] [Git][med-team/toil][master] document that toil in Debian is Py3 only
Michael R. Crusoe pushed to branch master at Debian Med / toil Commits: 397f6a52 by Michael R. Crusoe at 2019-01-07T12:59:51Z document that toil in Debian is Py3 only - - - - - 1 changed file: - debian/changelog Changes: = debian/changelog = @@ -1,6 +1,7 @@ toil (3.18.0-1) UNRELEASED; urgency=medium - * New upstream version. + * New upstream version; switch to Python3 only due to cwltool being py3 in +Debian. * skip galaxy-lib, not yet packaged for Debian * Adjust docs for a Debian installed Toil. * cgcloud is no longer needed (moved into Toil itself). View it on GitLab: https://salsa.debian.org/med-team/toil/commit/397f6a52a6fead4fc608e146be12e13611efb1b3 -- View it on GitLab: https://salsa.debian.org/med-team/toil/commit/397f6a52a6fead4fc608e146be12e13611efb1b3 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/toil][master] 13 commits: skip galaxy-lib, not yet packaged for Debian
Michael R. Crusoe pushed to branch master at Debian Med / toil Commits: ee60b837 by Michael R. Crusoe at 2019-01-07T10:04:13Z skip galaxy-lib, not yet packaged for Debian - - - - - 6302fee8 by Michael R. Crusoe at 2019-01-07T10:31:40Z fix doc build - - - - - 1f2f49b3 by Michael R. Crusoe at 2019-01-07T10:47:12Z Adjust docs for a Debian installed Toil. - - - - - cf924632 by Michael R. Crusoe at 2019-01-07T10:52:51Z more missing deps - - - - - 46d02fb7 by Michael R. Crusoe at 2019-01-07T10:54:53Z New upstream version 3.18.0 - - - - - 6d56cbba by Michael R. Crusoe at 2019-01-07T10:55:03Z Update upstream source from tag upstream/3.18.0 Update to upstream version 3.18.0 with Debian dir edf8f711b582380aed6ca6f96befa1ceeb8b18e2 - - - - - 1689c770 by Michael R. Crusoe at 2019-01-07T11:07:34Z Update patches for 3.18.0 - - - - - 32dd207a by Michael R. Crusoe at 2019-01-07T11:13:01Z try building for Python 3 - - - - - 1e5a132b by Michael R. Crusoe at 2019-01-07T11:19:07Z cgcloud is no longer needed (moved into Toil itself). - - - - - 009d8c47 by Michael R. Crusoe at 2019-01-07T12:22:12Z adjust to newer cwltool - - - - - 37d9aed9 by Michael R. Crusoe at 2019-01-07T12:26:17Z Dont ship cwltoil, use toil-cwl-runner instead. - - - - - cd3bade7 by Michael R. Crusoe at 2019-01-07T12:35:12Z better document the patches - - - - - dc9c6567 by Michael R. Crusoe at 2019-01-07T12:46:10Z Fix spelling. - - - - - 30 changed files: - .gitignore - Makefile - README.rst - attic/toil-sort-example.py - debian/changelog - debian/clean - debian/control - + debian/patches/adjust_to_newer_cwltool - + debian/patches/debianize_docs - + debian/patches/no_galaxy_lib - debian/patches/no_virtualenv_to_create_manpages.patch - debian/patches/series - debian/patches/setting_version.patch - + debian/patches/spelling - debian/patches/version.patch - debian/rules - docs/appendices/environment_vars.rst - docs/contributing/contributing.rst - docs/developingWorkflows/developing.rst - docs/developingWorkflows/toilAPIBatchsystem.rst - docs/developingWorkflows/toilAPIFilestore.rst - docs/gettingStarted/install.rst - docs/gettingStarted/quickStart.rst - docs/running/cliOptions.rst - docs/running/cloud/amazon.rst - docs/running/cloud/azure.rst - docs/running/cloud/clusterUtils.rst - docs/running/cloud/gce.rst - docs/running/cwl.rst - docs/running/hpcEnvironments.rst The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/toil/compare/faad0bfc68d9b1c0e1ac367172561f3c90474760...dc9c65671624eef6b331259c906cf34714492a5f -- View it on GitLab: https://salsa.debian.org/med-team/toil/compare/faad0bfc68d9b1c0e1ac367172561f3c90474760...dc9c65671624eef6b331259c906cf34714492a5f You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/toil] Pushed new tag upstream/3.18.0
Michael R. Crusoe pushed new tag upstream/3.18.0 at Debian Med / toil -- View it on GitLab: https://salsa.debian.org/med-team/toil/tree/upstream/3.18.0 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/toil][pristine-tar] pristine-tar data for toil_3.18.0.orig.tar.gz
Michael R. Crusoe pushed to branch pristine-tar at Debian Med / toil Commits: ef7c43dc by Michael R. Crusoe at 2019-01-07T10:55:03Z pristine-tar data for toil_3.18.0.orig.tar.gz - - - - - 2 changed files: - + toil_3.18.0.orig.tar.gz.delta - + toil_3.18.0.orig.tar.gz.id Changes: = toil_3.18.0.orig.tar.gz.delta = Binary files /dev/null and b/toil_3.18.0.orig.tar.gz.delta differ = toil_3.18.0.orig.tar.gz.id = @@ -0,0 +1 @@ +a3cb65bb03d8e166d4c9b614f607e58fd0bdd260 View it on GitLab: https://salsa.debian.org/med-team/toil/commit/ef7c43dcd484c9bf5d6ae277341ac711b3df7857 -- View it on GitLab: https://salsa.debian.org/med-team/toil/commit/ef7c43dcd484c9bf5d6ae277341ac711b3df7857 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/toil][upstream] New upstream version 3.18.0
Michael R. Crusoe pushed to branch upstream at Debian Med / toil Commits: 46d02fb7 by Michael R. Crusoe at 2019-01-07T10:54:53Z New upstream version 3.18.0 - - - - - 30 changed files: - .gitignore - Makefile - README.rst - attic/toil-sort-example.py - docs/appendices/environment_vars.rst - docs/contributing/contributing.rst - docs/developingWorkflows/developing.rst - docs/developingWorkflows/toilAPIBatchsystem.rst - docs/developingWorkflows/toilAPIFilestore.rst - docs/gettingStarted/install.rst - docs/gettingStarted/quickStart.rst - docs/running/cliOptions.rst - docs/running/cloud/amazon.rst - docs/running/cloud/azure.rst - docs/running/cloud/clusterUtils.rst - docs/running/cloud/gce.rst - docs/running/cwl.rst - docs/running/hpcEnvironments.rst - docs/running/introduction.rst - docs/running/wdl.rst - setup.cfg - setup.py - src/toil/__init__.py - src/toil/batchSystems/abstractGridEngineBatchSystem.py - src/toil/batchSystems/gridengine.py - src/toil/batchSystems/htcondor.py - src/toil/batchSystems/lsf.py - src/toil/batchSystems/lsfHelper.py - src/toil/batchSystems/mesos/batchSystem.py - src/toil/batchSystems/options.py The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/toil/commit/46d02fb72358d33f4a73f83ba4b22d46ec8ecb04 -- View it on GitLab: https://salsa.debian.org/med-team/toil/commit/46d02fb72358d33f4a73f83ba4b22d46ec8ecb04 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/toil][master] 2 commits: debhelper 11
Michael R. Crusoe pushed to branch master at Debian Med / toil Commits: 07057d81 by Michael R. Crusoe at 2019-01-07T13:02:51Z debhelper 11 - - - - - c342c91f by Michael R. Crusoe at 2019-01-07T13:04:21Z Standards-Version: 4.3.0 (no changes needed). - - - - - 3 changed files: - debian/changelog - debian/compat - debian/control Changes: = debian/changelog = @@ -7,6 +7,8 @@ toil (3.18.0-1) UNRELEASED; urgency=medium * cgcloud is no longer needed (moved into Toil itself). * Add patch to adjust to newer version of the CWL reference runner. * Fix spelling. + * debhelper 11 + * Standards-Version: 4.3.0 (no changes needed). -- Michael R. Crusoe Mon, 07 Jan 2019 02:04:03 -0800 = debian/compat = @@ -1 +1 @@ -9 +11 = debian/control = @@ -4,7 +4,7 @@ Priority: optional Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Michael R. Crusoe -Build-Depends: debhelper (>= 10), +Build-Depends: debhelper (>= 11~), dh-python, python3-all, python3-setuptools, @@ -16,11 +16,10 @@ Build-Depends: debhelper (>= 10), python3-urllib3, python3-chardet, python3-sphinx -Standards-Version: 4.1.4 +Standards-Version: 4.3.0 Homepage: https://github.com/BD2KGenomics/toil Vcs-Git: https://salsa.debian.org/med-team/toil.git Vcs-Browser: https://salsa.debian.org/med-team/toil -#Testsuite: autopkgtest-pkg-python Package: toil Architecture: all View it on GitLab: https://salsa.debian.org/med-team/toil/compare/397f6a52a6fead4fc608e146be12e13611efb1b3...c342c91fb72d173c285ad6592cf18167cda027a2 -- View it on GitLab: https://salsa.debian.org/med-team/toil/compare/397f6a52a6fead4fc608e146be12e13611efb1b3...c342c91fb72d173c285ad6592cf18167cda027a2 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/khmer] Pushed new tag debian/2.1.2+dfsg-5
Michael R. Crusoe pushed new tag debian/2.1.2+dfsg-5 at Debian Med / khmer -- View it on GitLab: https://salsa.debian.org/med-team/khmer/tree/debian/2.1.2+dfsg-5 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/trinityrnaseq] Pushed new tag debian/2.6.6+dfsg-6
Michael R. Crusoe pushed new tag debian/2.6.6+dfsg-6 at Debian Med / trinityrnaseq -- View it on GitLab: https://salsa.debian.org/med-team/trinityrnaseq/tree/debian/2.6.6+dfsg-6 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/python-schema-salad][master] Fix the already shipped tests and enable them as autopkgtests.
Michael R. Crusoe pushed to branch master at Debian Med / python-schema-salad
Commits:
71279ade by Michael R. Crusoe at 2019-01-04T14:45:42Z
Fix the already shipped tests and enable them as autopkgtests.
- - - - -
6 changed files:
- debian/changelog
- debian/control
- debian/patches/exec_cwl
- debian/rules
- + debian/tests/control
- + debian/tests/run-tests
Changes:
=
debian/changelog
=
@@ -1,3 +1,10 @@
+python-schema-salad (3.0.20181206233650-2) unstable; urgency=medium
+
+ * Fix the already shipped tests and enable them as autopkgtests.
+ * Run the same tests at compile time.
+
+ -- Michael R. Crusoe Fri, 04 Jan 2019 06:45:22
-0800
+
python-schema-salad (3.0.20181206233650-1) unstable; urgency=medium
* New upstream version
=
debian/control
=
@@ -2,7 +2,6 @@ Source: python-schema-salad
Maintainer: Debian Med Packaging Team
Uploaders: Michael R. Crusoe
Section: python
-Testsuite: autopkgtest-pkg-python
Priority: optional
Build-Depends: debhelper (>= 11~),
dh-python,
@@ -18,6 +17,8 @@ Build-Depends: debhelper (>= 11~),
python3-cachecontrol,
python3-lockfile,
python3-typing-extensions,
+ python3-pytest-xdist,
+ python3-pytest-runner,
help2man
Standards-Version: 4.3.0
Vcs-Browser: https://salsa.debian.org/med-team/python-schema-salad
=
debian/patches/exec_cwl
=
@@ -285,3 +285,61 @@ Subject: Add proper "#!" header to all CWL files
-out: [out]
\ No newline at end of file
+out: [out]
+--- schema-salad.orig/schema_salad/tests/test_print_oneline.py
schema-salad/schema_salad/tests/test_print_oneline.py
+@@ -46,7 +46,7 @@
+ except RuntimeError as e:
+ msg =
reformat_yaml_exception_message(strip_dup_lineno(six.text_type(e)))
+ msg = to_one_line_messages(msg)
+-self.assertTrue(msg.endswith(src+":10:1: could not find
expected \':\'"))
++self.assertTrue(msg.endswith(src+":11:1: could not find
expected \':\'"))
+ print("\n", e)
+ raise
+
+@@ -62,10 +62,9 @@
+
six.text_type(get_data("tests/test_schema/"+src)), True)
+ except ValidationException as e:
+ msgs = to_one_line_messages(str(e)).splitlines()
+-self.assertEqual(len(msgs), 3)
+-self.assertTrue(msgs[0].endswith(src+":9:1: the `outputs`
field is not valid because"))
+-self.assertTrue(msgs[1].endswith(src+":13:5: missing required
field `id`"))
+-self.assertTrue(msgs[2].endswith(src+":13:5: invalid field
`aa`, expected one of: 'label', 'secondaryFiles', 'format', 'streamable',
'doc', 'id', 'outputBinding', 'type'"))
++assert len(msgs) == 2, msgs
++self.assertTrue(msgs[0].endswith(src+":14:5: missing required
field `id`"))
++self.assertTrue(msgs[1].endswith(src+":14:5: invalid field
`aa`, expected one of: 'label', 'secondaryFiles', 'format', 'streamable',
'doc', 'id', 'outputBinding', 'type'"))
+ print("\n", e)
+ raise
+
+@@ -88,9 +87,9 @@
+ self.assertEqual(len(msgs), 2)
+ print("\n", e)
+ assert msgs[0].endswith(
+-src + ':8:1: checking field `outputs`')
++src + ':9:1: checking field `outputs`')
+ assert msgs[1].endswith(
+-src + ':13:5: Field `type` references unknown identifier '
++src + ':14:5: Field `type` references unknown identifier '
+ '`Filea`, tried file://%s#Filea' % (fullpath))
+ raise
+
+@@ -108,8 +107,8 @@
+ msg =
reformat_yaml_exception_message(strip_dup_lineno(six.text_type(e)))
+ msgs = msg.splitlines()
+ self.assertEqual(len(msgs), 2)
+-self.assertTrue(msgs[0].endswith(src+":9:7: while scanning a
simple key"))
+-self.assertTrue(msgs[1].endswith(src+":10:1: could not find
expected ':'"))
++self.assertTrue(msgs[0].endswith(src+":10:7: while scanning a
simple key"))
++self.assertTrue(msgs[1].endswith(src+":11:1: could not find
expected ':'"))
+ print("\n", e)
+ raise
+
+@@ -125,7 +124,7 @@
+
six.text_type(get_data("tests/test_schema/"+src)), True)
+ except Runti
[med-svn] [Git][med-team/python-schema-salad][master] patch sent upstream (to me)
Michael R. Crusoe pushed to branch master at Debian Med / python-schema-salad Commits: 7828f97f by Michael R. Crusoe at 2019-01-04T15:19:15Z patch sent upstream (to me) - - - - - 1 changed file: - debian/patches/exec_cwl Changes: = debian/patches/exec_cwl = @@ -1,5 +1,6 @@ From: Michael R. Crusoe Subject: Add proper "#!" header to all CWL files +Forwarded: https://github.com/common-workflow-language/schema_salad/pull/225 --- schema-salad.orig/schema_salad/tests/foreign/foreign_prop1.cwl +++ schema-salad/schema_salad/tests/foreign/foreign_prop1.cwl @@ -1,3 +1,4 @@ View it on GitLab: https://salsa.debian.org/med-team/python-schema-salad/commit/7828f97fd1393f55a3639cc008794a7ebcc9fa77 -- View it on GitLab: https://salsa.debian.org/med-team/python-schema-salad/commit/7828f97fd1393f55a3639cc008794a7ebcc9fa77 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/rapmap][master] Upload to unstable.
Michael R. Crusoe pushed to branch master at Debian Med / rapmap
Commits:
cb8fbe48 by Michael R. Crusoe at 2019-01-02T11:07:16Z
Upload to unstable.
- - - - -
1 changed file:
- debian/changelog
Changes:
=
debian/changelog
=
@@ -1,10 +1,10 @@
-rapmap (0.12.0+dfsg-3) UNRELEASED; urgency=medium
+rapmap (0.12.0+dfsg-3) unstable; urgency=medium
* debian/patches/portable_pause: add ppc64el and arm64 alternatives to
asm("pause").
* debian/patches/no_gomp_needed: Avoid unnecessary linkage to gomp.
- -- Michael R. Crusoe Tue, 01 Jan 2019 08:09:15
-0800
+ -- Michael R. Crusoe Wed, 02 Jan 2019 03:07:04
-0800
rapmap (0.12.0+dfsg-2) unstable; urgency=medium
View it on GitLab:
https://salsa.debian.org/med-team/rapmap/commit/cb8fbe48d869f1a526239944d6e14d640367b47d
--
View it on GitLab:
https://salsa.debian.org/med-team/rapmap/commit/cb8fbe48d869f1a526239944d6e14d640367b47d
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[med-svn] [Git][med-team/rapmap] Pushed new tag debian/0.12.0+dfsg-3
Michael R. Crusoe pushed new tag debian/0.12.0+dfsg-3 at Debian Med / rapmap -- View it on GitLab: https://salsa.debian.org/med-team/rapmap/tree/debian/0.12.0+dfsg-3 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/staden-io-lib][master] Upload to unstable.
Michael R. Crusoe pushed to branch master at Debian Med / staden-io-lib Commits: 89bb5ae9 by Michael R. Crusoe at 2019-01-02T11:09:04Z Upload to unstable. - - - - - 1 changed file: - debian/changelog Changes: = debian/changelog = @@ -1,11 +1,11 @@ -staden-io-lib (1.14.11-6) UNRELEASED; urgency=medium +staden-io-lib (1.14.11-6) unstable; urgency=medium * Switch to -O0 on armhf, mips. Closes: #916262 * Standards-Version: 4.3.0 * debian/control: mark staden-io-lib-examples as Multi-Arch: foreign - * changelog & debian/patches/spelling: spelling (independent) + * changelog & debian/patches/spelling: typo fix (independent) - -- Michael R. Crusoe Tue, 01 Jan 2019 01:26:00 -0800 + -- Michael R. Crusoe Wed, 02 Jan 2019 03:08:23 -0800 staden-io-lib (1.14.11-5) unstable; urgency=medium View it on GitLab: https://salsa.debian.org/med-team/staden-io-lib/commit/89bb5ae90a02ca7f5c69001499e85305688c4427 -- View it on GitLab: https://salsa.debian.org/med-team/staden-io-lib/commit/89bb5ae90a02ca7f5c69001499e85305688c4427 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/staden-io-lib] Pushed new tag debian/1.14.11-6
Michael R. Crusoe pushed new tag debian/1.14.11-6 at Debian Med / staden-io-lib -- View it on GitLab: https://salsa.debian.org/med-team/staden-io-lib/tree/debian/1.14.11-6 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/seqan2][master] Fix thread wait assembly for IA64.
Michael R. Crusoe pushed to branch master at Debian Med / seqan2
Commits:
aebeb222 by Michael R. Crusoe at 2019-01-02T12:28:56Z
Fix thread wait assembly for IA64.
- - - - -
3 changed files:
- debian/changelog
- + debian/patches/ia64_yield
- debian/patches/series
Changes:
=
debian/changelog
=
@@ -1,3 +1,10 @@
+seqan2 (2.4.0+dfsg-10) UNRELEASED; urgency=medium
+
+ * debian/patches/ia64_yield: Fix thread wait assembly for IA64.
+Closes: #890185
+
+ -- Michael R. Crusoe Wed, 02 Jan 2019 03:47:37
-0800
+
seqan2 (2.4.0+dfsg-9) unstable; urgency=medium
[ Michael R. Crusoe ]
=
debian/patches/ia64_yield
=
@@ -0,0 +1,13 @@
+From: Michael R. Crusoe
+Subject: Fix thread wait for IA64
+--- seqan2.orig/include/seqan/parallel/parallel_lock.h
seqan2/include/seqan/parallel/parallel_lock.h
+@@ -233,6 +233,8 @@
+ __asm__ __volatile__ ("or 27,27,27" ::: "memory");
+ #elif defined(__SSE2__) // AMD and Intel
+ _mm_pause();
++#elif defined(__ia64__) // IA64
++__asm__ __volatile__ ("hint @pause");
+ #else // everything else.
+ asm volatile ("nop" ::: "memory"); // default operation - does nothing
=> Might lead to passive spinning.
+ #endif
=
debian/patches/series
=
@@ -7,3 +7,4 @@ install_fiona_illumina
ctdVersion.patch
fix_manpage_formatting.patch
no-unaligned-access.patch
+ia64_yield
View it on GitLab:
https://salsa.debian.org/med-team/seqan2/commit/aebeb22264f6219e76473967cc5caa131aac65e6
--
View it on GitLab:
https://salsa.debian.org/med-team/seqan2/commit/aebeb22264f6219e76473967cc5caa131aac65e6
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[med-svn] [Git][med-team/hhsuite][master] update upstream URL
Michael R. Crusoe pushed to branch master at Debian Med / hhsuite Commits: 7023c65c by Michael R. Crusoe at 2019-01-04T17:20:21Z update upstream URL - - - - - 1 changed file: - debian/control Changes: = debian/control = @@ -15,7 +15,7 @@ Build-Depends: debhelper (>= 10), Standards-Version: 4.2.0 Vcs-Browser: https://salsa.debian.org/med-team/hhsuite Vcs-Git: https://salsa.debian.org/med-team/hhsuite.git -Homepage: http://toolkit.genzentrum.lmu.de/sections/search +Homepage: https://toolkit.tuebingen.mpg.de/ Package: hhsuite Architecture: amd64 View it on GitLab: https://salsa.debian.org/med-team/hhsuite/commit/7023c65c4fb9a0bcbcec479d1f39f02f2e440411 -- View it on GitLab: https://salsa.debian.org/med-team/hhsuite/commit/7023c65c4fb9a0bcbcec479d1f39f02f2e440411 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libthread-pool][master] 2 commits: add missing pthread
Michael R. Crusoe pushed to branch master at Debian Med / libthread-pool
Commits:
964266ed by Michael R. Crusoe at 2019-01-04T17:44:33Z
add missing pthread
- - - - -
3c785962 by Michael R. Crusoe at 2019-01-04T17:44:46Z
Remove trailing whitespace in debian/copyright
- - - - -
4 changed files:
- debian/changelog
- debian/control
- debian/copyright
- debian/rules
Changes:
=
debian/changelog
=
@@ -1,3 +1,11 @@
+libthread-pool (1.0.0-3) UNRELEASED; urgency=medium
+
+ * Team upload.
+ * Add missing '-pthread'
+ * Remove trailing whitespace in debian/copyright
+
+ -- Michael R. Crusoe Fri, 04 Jan 2019 09:44:11
-0800
+
libthread-pool (1.0.0-2) unstable; urgency=medium
* Do not build with -march=native
=
debian/control
=
@@ -8,7 +8,7 @@ Build-Depends: debhelper (>= 11~),
d-shlibs,
rename,
libgtest-dev
-Standards-Version: 4.2.0
+Standards-Version: 4.3.0
Vcs-Browser: https://salsa.debian.org/med-team/libthread-pool
Vcs-Git: https://salsa.debian.org/med-team/libthread-pool.git
Homepage: https://github.com/rvaser/libthread-pool
@@ -31,8 +31,7 @@ Description: C++ thread pool library
Package: libthread-pool-dev
Architecture: any
Section: libdevel
-Depends: ${shlibs:Depends},
- ${misc:Depends},
+Depends: ${misc:Depends},
libthread-pool0 (= ${binary:Version})
Description: C++ thread pool library (devel)
A thread pool is a software design pattern for achieving concurrency of
=
debian/copyright
=
@@ -1,6 +1,6 @@
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: thread_pool
-Upstream-Contact:
+Upstream-Contact:
Source: https://github.com/rvaser/thread_pool/releases
Files: *
=
debian/rules
=
@@ -3,7 +3,7 @@
# DH_VERBOSE := 1
export DEB_BUILD_MAINT_OPTIONS=hardening=+all
-
+export DEB_LDFLAGS_MAINT_APPEND+=-pthread
%:
dh $@
View it on GitLab:
https://salsa.debian.org/med-team/libthread-pool/compare/83af403eadaa67cfa6ac03cf3c3dbcf2c6d24ffa...3c7859620f1255bf119d6acf036e0a13a2382570
--
View it on GitLab:
https://salsa.debian.org/med-team/libthread-pool/compare/83af403eadaa67cfa6ac03cf3c3dbcf2c6d24ffa...3c7859620f1255bf119d6acf036e0a13a2382570
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[med-svn] [Git][med-team/libbpp-phyl][master] libbpp-phyl-dev: Multi-Arch: same
Michael R. Crusoe pushed to branch master at Debian Med / libbpp-phyl
Commits:
52aa77b4 by Michael R. Crusoe at 2019-01-04T18:36:07Z
libbpp-phyl-dev: Multi-Arch: same
Remove trailing whitespace in debian/copyright
add missing ${devlibs:Depends}
- - - - -
3 changed files:
- debian/changelog
- debian/control
- debian/copyright
Changes:
=
debian/changelog
=
@@ -1,8 +1,14 @@
libbpp-phyl (2.4.1-2) UNRELEASED; urgency=medium
+ [ Jelmer Vernooij ]
* Use secure copyright file specification URI.
* Trim trailing whitespace.
+ [ Michael R. Crusoe ]
+ * libbpp-phyl-dev: Multi-Arch: same & add missing ${devlibs:Depends}
+ * Remove trailing whitespace in debian/copyright
+ * Standards-Version: 4.3.0
+
-- Jelmer Vernooij Wed, 24 Oct 2018 22:53:13 +
libbpp-phyl (2.4.1-1) unstable; urgency=medium
=
debian/control
=
@@ -8,16 +8,18 @@ Build-Depends: debhelper (>= 11~),
cmake,
d-shlibs (>= 0.82),
libbpp-seq-dev (>= 2.4.1)
-Standards-Version: 4.2.0
+Standards-Version: 4.3.0
Vcs-Browser: https://salsa.debian.org/med-team/libbpp-phyl
Vcs-Git: https://salsa.debian.org/med-team/libbpp-phyl.git
Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
Package: libbpp-phyl-dev
Architecture: any
+Multi-Arch: same
Section: libdevel
Depends: libbpp-phyl12 (= ${binary:Version}),
${misc:Depends},
+${devlibs:Depends},
libbpp-seq-dev (>= 2.4.1)
Description: Bio++ Phylogenetic library development files
Bio++ is a set of C++ libraries for Bioinformatics, including sequence
=
debian/copyright
=
@@ -19,7 +19,7 @@ License: GPL-2+
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
- .
+ .
This package is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
@@ -159,7 +159,7 @@ License: CeCILL
.
The purpose of the Agreement is the grant by the Licensor to the
Licensee of a non-exclusive, transferable and worldwide license for the
- Software as set forth in Article 5 hereinafter for the whole term of the
+ Software as set forth in Article 5 hereinafter for the whole term of the
protection granted by the rights over said Software.
.
.
@@ -179,7 +179,7 @@ License: CeCILL
characteristics of the Software, to the limited warranty, and to the
fact that its use is restricted to experienced users has been provided
to the Licensee prior to its acceptance as set forth in Article 3.1
- hereinabove, and the Licensee hereby acknowledges that it has read and
+ hereinabove, and the Licensee hereby acknowledges that it has read and
understood it.
.
.
@@ -427,7 +427,7 @@ License: CeCILL
9.3 The Licensee acknowledges that the Software is supplied "as is" by
the Licensor without any other express or tacit warranty, other than
that provided for in Article 9.2 and, in particular, without any warranty
- as to its commercial value, its secured, safe, innovative or relevant
+ as to its commercial value, its secured, safe, innovative or relevant
nature.
.
Specifically, the Licensor does not warrant that the Software is free
View it on GitLab:
https://salsa.debian.org/med-team/libbpp-phyl/commit/52aa77b49eb37241b7c0b7b02594d9369498f2f9
--
View it on GitLab:
https://salsa.debian.org/med-team/libbpp-phyl/commit/52aa77b49eb37241b7c0b7b02594d9369498f2f9
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[med-svn] [Git][med-team/libpsortb][master] 2 commits: Upload to unstable
Michael R. Crusoe pushed to branch master at Debian Med / libpsortb
Commits:
ed2c60db by Michael R. Crusoe at 2019-01-04T18:45:04Z
Upload to unstable
- - - - -
b60043bb by Michael R. Crusoe at 2019-01-04T19:18:56Z
put -lsvm in the correct location
Broken until https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=918251 is
fixed.
- - - - -
3 changed files:
- debian/changelog
- debian/control
- debian/patches/use_debian_packaged_libsvm.patch
Changes:
=
debian/changelog
=
@@ -1,3 +1,9 @@
+libpsortb (1.0+dfsg-3) unstable; urgency=medium
+
+ * Team upload.
+
+ -- Michael R. Crusoe Fri, 04 Jan 2019 10:43:39
-0800
+
libpsortb (1.0+dfsg-2) unstable; urgency=medium
* debhelper 11
=
debian/control
=
@@ -6,10 +6,10 @@ Priority: optional
Build-Depends: debhelper (>= 11~),
d-shlibs,
libsvm-dev,
- libsquid-dev (>= 1.9g+cvs20050121-9~),
- libhmmer2-dev (>= 2.3.2+dfsg-2~),
+ libsquid-dev,
+ libhmmer2-dev,
pkg-config
-Standards-Version: 4.2.1
+Standards-Version: 4.3.0
Vcs-Browser: https://salsa.debian.org/med-team/libpsortb
Vcs-Git: https://salsa.debian.org/med-team/libpsortb.git
Homepage: http://www.psort.org/
@@ -37,7 +37,6 @@ Package: libmodhmm-dev
Architecture: any
Section: libdevel
Depends: libmodhmm0 (= ${binary:Version}),
- ${shlibs:Depends},
${misc:Depends}
Description: library for constructing, training and scoring hidden Markov
models (dev)
Library for constructing, training and scoring hidden Markov models. It
@@ -84,7 +83,6 @@ Architecture: any
Section: libdevel
Depends: libsvmloc0 (= ${binary:Version}),
libsvm-dev,
- ${shlibs:Depends},
${misc:Depends}
Description: PSORTb adapted library for svm machine-learning library (dev)
Libsvm is a machine-learning library which is an easy-to-use package
=
debian/patches/use_debian_packaged_libsvm.patch
=
@@ -2,22 +2,21 @@ Author: Andreas Tille
Last-Update: Fri, 17 Mar 2017 10:23:15 +010
Description: Use Debian packaged libsvm
a/svmloc/Makefile.am
-+++ b/svmloc/Makefile.am
-@@ -3,8 +3,8 @@
+--- libpsortb.orig/svmloc/Makefile.am
libpsortb/svmloc/Makefile.am
+@@ -3,8 +3,5 @@
# svmloc dir
lib_LTLIBRARIES = libsvmloc.la
-libsvmloc_la_SOURCES = binding.cpp libsvm.cpp svmloc.cpp binding.h libsvm.h
svmloc.h
-+libsvmloc_la_SOURCES = binding.cpp svmloc.cpp binding.h svmloc.h
- libsvmloc_la_LDFLAGS = -version-info 0:0:0
-
+-libsvmloc_la_LDFLAGS = -version-info 0:0:0
+-
-noinst_HEADERS = \
-COPYRIGHT
-+LDADD = -lsvm
-+
a/svmloc/svmloc.h
-+++ b/svmloc/svmloc.h
++libsvmloc_la_SOURCES = binding.cpp svmloc.cpp binding.h svmloc.h
++libsvmloc_la_LDFLAGS = -version-info 0:0:0 -lsvm
+--- libpsortb.orig/svmloc/svmloc.h
libpsortb/svmloc/svmloc.h
@@ -12,7 +12,7 @@
#include
#include
@@ -27,9 +26,9 @@ Description: Use Debian packaged libsvm
using namespace std;
a/svmloc/svmloc.cpp
-+++ b/svmloc/svmloc.cpp
-@@ -166,7 +166,7 @@ int SVM::train(int retrain) {
+--- libpsortb.orig/svmloc/svmloc.cpp
libpsortb/svmloc/svmloc.cpp
+@@ -166,7 +166,7 @@
// Free any old model we have.
if(model != NULL) {
@@ -38,7 +37,7 @@ Description: Use Debian packaged libsvm
model = NULL;
}
-@@ -282,7 +282,7 @@ int SVM::loadModel(char *filename) {
+@@ -282,7 +282,7 @@
}
if(model != NULL) {
@@ -47,7 +46,7 @@ Description: Use Debian packaged libsvm
model = NULL;
}
-@@ -436,7 +436,7 @@ double SVM::crossValidate(int nfolds) {
+@@ -436,7 +436,7 @@
sumyy += y*y;
sumvy += v*y;
}
@@ -56,7 +55,7 @@ Description: Use Debian packaged libsvm
// cout << "Mean squared error = %g\n", error/(end-begin));
total_error += error;
} else {
-@@ -447,7 +447,7 @@ double SVM::crossValidate(int nfolds) {
+@@ -447,7 +447,7 @@
double v = svm_predict(submodel,prob->x[j]);
if(v == prob->y[j]) ++correct;
}
@@ -65,7 +64,7 @@ Description: Use Debian packaged libsvm
//cout << "Accuracy = " << 100.0*correct/(end-begin) << " (" <<
//correct << "/" << (end-begin) << endl;
total_correct += correct;
-@@ -502,6 +502,6 @@ int SVM::checkProbabilityModel() {
+@@ -502,6 +502,6 @@
SVM::~SVM() {
if(x_space!=NULL) { free_x_space(); }
View it on GitLab:
https://salsa.debian.org/med-team/libpsortb/compare/6a5f0e2d7bdc5d848fddda4aab6f69d1c8172e6a...b60043bb5a4fc2fd2c514759b91932875b0025f7
--
View it on GitLab:
https://salsa.debian.org/med-team/libpsortb/compare/6a5f0e2d7bdc5d848fddda4aab6f69d1c8172e6a...b60043bb5
[med-svn] [Git][med-team/spdlog][master] 5 commits: New upstream version 1.3.0
Michael R. Crusoe pushed to branch master at Debian Med / spdlog Commits: 813e61d2 by Michael R. Crusoe at 2019-01-12T13:33:36Z New upstream version 1.3.0 - - - - - 36a5de47 by Michael R. Crusoe at 2019-01-12T13:33:37Z Update upstream source from tag upstream/1.3.0 Update to upstream version 1.3.0 with Debian dir aeac778fc417acbac6f34a59660ac942bacae8ce - - - - - 6ccab356 by Michael R. Crusoe at 2019-01-12T13:33:37Z New upstream version - - - - - c96a7802 by Michael R. Crusoe at 2019-01-12T14:11:53Z build the benchmark, update Standards-Version - - - - - 9e423a29 by Michael R. Crusoe at 2019-01-12T14:52:38Z upload to unstable. - - - - - 30 changed files: - .clang-format - .travis.yml - CMakeLists.txt - README.md - appveyor.yml - bench/CMakeLists.txt - bench/Makefile - bench/async_bench.cpp - bench/bench.cpp - + bench/formatter-bench.cpp - bench/latency.cpp - − bench/spdlog-async.cpp - cmake/Config.cmake.in - debian/changelog - debian/control - debian/docs - + debian/examples - debian/rules - example/example.cpp - example/example.vcxproj - + example/logs/.gitignore - example/multisink.cpp - include/spdlog/async.h - include/spdlog/common.h - include/spdlog/details/async_logger_impl.h - include/spdlog/details/file_helper.h - include/spdlog/details/fmt_helper.h - include/spdlog/details/log_msg.h - include/spdlog/details/logger_impl.h - include/spdlog/details/os.h The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/spdlog/compare/82566615cd49e953405f94329848ff24d2f7a38f...9e423a29f0aa1508c60fd01416bcc670fb84830c -- View it on GitLab: https://salsa.debian.org/med-team/spdlog/compare/82566615cd49e953405f94329848ff24d2f7a38f...9e423a29f0aa1508c60fd01416bcc670fb84830c You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/spdlog][upstream] New upstream version 1.3.0
Michael R. Crusoe pushed to branch upstream at Debian Med / spdlog Commits: 813e61d2 by Michael R. Crusoe at 2019-01-12T13:33:36Z New upstream version 1.3.0 - - - - - 30 changed files: - .clang-format - .travis.yml - CMakeLists.txt - README.md - appveyor.yml - bench/CMakeLists.txt - bench/Makefile - bench/async_bench.cpp - bench/bench.cpp - + bench/formatter-bench.cpp - bench/latency.cpp - − bench/spdlog-async.cpp - cmake/Config.cmake.in - example/example.cpp - example/example.vcxproj - example/multisink.cpp - include/spdlog/async.h - include/spdlog/common.h - include/spdlog/details/async_logger_impl.h - include/spdlog/details/file_helper.h - include/spdlog/details/fmt_helper.h - include/spdlog/details/log_msg.h - include/spdlog/details/logger_impl.h - include/spdlog/details/os.h - include/spdlog/details/pattern_formatter.h - include/spdlog/details/periodic_worker.h - include/spdlog/details/registry.h - include/spdlog/details/thread_pool.h - include/spdlog/fmt/bin_to_hex.h - + include/spdlog/fmt/bundled/chrono.h The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/spdlog/commit/813e61d2e1ec63549124f7d9c8f453b7116a13aa -- View it on GitLab: https://salsa.debian.org/med-team/spdlog/commit/813e61d2e1ec63549124f7d9c8f453b7116a13aa You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/spdlog] Pushed new tag upstream/1.3.0
Michael R. Crusoe pushed new tag upstream/1.3.0 at Debian Med / spdlog -- View it on GitLab: https://salsa.debian.org/med-team/spdlog/tree/upstream/1.3.0 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/spdlog] Pushed new tag debian/1.3.0-1
Michael R. Crusoe pushed new tag debian/1.3.0-1 at Debian Med / spdlog -- View it on GitLab: https://salsa.debian.org/med-team/spdlog/tree/debian/1.3.0-1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/spdlog][pristine-tar] pristine-tar data for spdlog_1.3.0.orig.tar.gz
Michael R. Crusoe pushed to branch pristine-tar at Debian Med / spdlog Commits: f62f6c0a by Michael R. Crusoe at 2019-01-12T13:33:37Z pristine-tar data for spdlog_1.3.0.orig.tar.gz - - - - - 2 changed files: - + spdlog_1.3.0.orig.tar.gz.delta - + spdlog_1.3.0.orig.tar.gz.id Changes: = spdlog_1.3.0.orig.tar.gz.delta = Binary files /dev/null and b/spdlog_1.3.0.orig.tar.gz.delta differ = spdlog_1.3.0.orig.tar.gz.id = @@ -0,0 +1 @@ +36dc22f4b66c3b9739ff1b4c5ce58d6ce2345386 View it on GitLab: https://salsa.debian.org/med-team/spdlog/commit/f62f6c0adff3eb63b16a0ff249588132645afa18 -- View it on GitLab: https://salsa.debian.org/med-team/spdlog/commit/f62f6c0adff3eb63b16a0ff249588132645afa18 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/spdlog][master] No point in building benchmarks
Michael R. Crusoe pushed to branch master at Debian Med / spdlog Commits: 556000e4 by Michael R. Crusoe at 2019-01-12T17:59:30Z No point in building benchmarks It causes issues on some unofficial archs. - - - - - 4 changed files: - debian/changelog - debian/control - + debian/lintian-overrides - debian/rules Changes: = debian/changelog = @@ -1,3 +1,10 @@ +spdlog (1:1.3.0-2) unstable; urgency=medium + + * No point in building benchmarks, causes issues on some unofficial +archs. + + -- Michael R. Crusoe Sat, 12 Jan 2019 09:59:25 -0800 + spdlog (1:1.3.0-1) unstable; urgency=medium * debian/control: Mark us as Multi-Arch: same. = debian/control = @@ -4,8 +4,7 @@ Uploaders: Michael R. Crusoe Section: libdevel Priority: optional Build-Depends: debhelper (>= 11~), - cmake, - libbenchmark-dev + cmake Standards-Version: 4.3.0 Vcs-Browser: https://salsa.debian.org/med-team/spdlog Vcs-Git: https://salsa.debian.org/med-team/spdlog.git = debian/lintian-overrides = @@ -0,0 +1 @@ +libspdlog-dev: package-contains-empty-directory usr/share/doc/libspdlog-dev/examples/logs/ = debian/rules = @@ -9,8 +9,8 @@ endif override_dh_auto_configure: dh_auto_configure -- -DSPDLOG_BUILD_EXAMPLES=ON \ - -DSPDLOG_BUILD_BENCH=ON \ - -DSPDLOG_BUILD_TESTS=ON \ + -DSPDLOG_BUILD_BENCH=OFF \ + -DSPDLOG_BUILD_TESTS=ON override_dh_auto_install: rm -f example/logs/.gitignore View it on GitLab: https://salsa.debian.org/med-team/spdlog/commit/556000e42372387f902a867fe5a7934f3b02cf9e -- View it on GitLab: https://salsa.debian.org/med-team/spdlog/commit/556000e42372387f902a867fe5a7934f3b02cf9e You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/spdlog] Pushed new tag debian/1.3.0-2
Michael R. Crusoe pushed new tag debian/1.3.0-2 at Debian Med / spdlog -- View it on GitLab: https://salsa.debian.org/med-team/spdlog/tree/debian/1.3.0-2 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/toil] Deleted tag debian/3.18.0-2
Michael R. Crusoe deleted tag debian/3.18.0-2 at Debian Med / toil -- You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/toil] Pushed new tag debian/3.18.0-2
Michael R. Crusoe pushed new tag debian/3.18.0-2 at Debian Med / toil -- View it on GitLab: https://salsa.debian.org/med-team/toil/tree/debian/3.18.0-2 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/toil][master] 2 commits: add/update debian/{TODO, README.source, README.debian}
Michael R. Crusoe pushed to branch master at Debian Med / toil
Commits:
b1230168 by Michael R. Crusoe at 2019-01-14T08:04:55Z
add/update debian/{TODO,README.source,README.debian}
- - - - -
1b603096 by Michael R. Crusoe at 2019-01-14T08:04:55Z
man: symlink _toil_worker to toil
- - - - -
6 changed files:
- debian/README.Debian
- debian/README.source
- + debian/TODO
- debian/changelog
- debian/control
- + debian/links
Changes:
=
debian/README.Debian
=
@@ -3,9 +3,6 @@ toil for Debian
This package is still preliminary since
* testing is not activated
- * it is awkward to have both python2 and python3 supported, left it with
python2
* manpages are missing
- * dependency on cgcloud https://github.com/BD2KGenomics/cgcloud not followed
which ruins tests
---
- Steffen Moeller Sat, 14 Jan 2017 13:43:23 +0100
+ -- Michael R. Crusoe Sun, 13 Jan 2019 23:25:16
-0800
=
debian/README.source
=
@@ -1,10 +1,10 @@
toil for Debian
---
-The current version the package was derived from what was uploaded to the
-pypi repository. This should be changed towards the gihub repository,
-except for a lack of tags that are not set for the latest versions
-available on Pypi.
+This initial package does not yet run the complete test suite as the Python3
+compatability of toil is recent.
- -- Steffen Moeller Fri, 13 Jan 2017 15:58:18 +0100
+The bulk of the manual testing is currently focused on the toil-cwl-runner
+using the docker.io package.
+ -- Michael R. Crusoe Sun, 13 Jan 2019 23:25:16
-0800
=
debian/TODO
=
@@ -0,0 +1,17 @@
+Ship the rest of the docs
+
+Continue to cherry-pick Python3 fixes for the tests from upstream
+
+Run the tests at package build time
+
+Adapt the tests into an AutoPkgTest
+
+Figure out how to have tests that depends on a functioning Docker service work
+at build time & AutoPkgTest time (needs root and we run the docker daemon
+ourselves?)
+
+Same as above but for singularity-container instead of docker.io
+
+package python3-mesos
+
+
=
debian/changelog
=
@@ -4,6 +4,8 @@ toil (3.18.0-2) unstable; urgency=medium
(Closes: #919228)
* Refined the package description, added 'Provides: cwl-runner'
* Remove the partial mesos support until python3-mesos is packaged
+ * Suggests: docker.io | singularity-container | docker-ce
+ * Added debian/TODO, updated debian/README.{debian,source}
-- Michael R. Crusoe Sun, 13 Jan 2019 23:25:16
-0800
=
debian/control
=
@@ -33,7 +33,7 @@ Recommends:
python3-libcloud
# for mesos support, but needs python3-mesos first
# python3-protobuf,
-Suggests: python3-azure, python3-azure-storage
+Suggests: docker.io | singularity-container | docker-ce, python3-azure,
python3-azure-storage
#Suggests: python-toil-doc
Description: cross-platform workflow engine
Toil is a scalable, efficient, cross-platform and easy-to-use workflow
=
debian/links
=
@@ -0,0 +1 @@
+/usr/share/man/man1/toil.1.gz /usr/share/man/man1/_toil_worker.1.gz
View it on GitLab:
https://salsa.debian.org/med-team/toil/compare/4028fdb2d11226d478e7296db766d4bdf8e815c0...1b603096cf70b04784a5d6d76cf7f738c03d0875
--
View it on GitLab:
https://salsa.debian.org/med-team/toil/compare/4028fdb2d11226d478e7296db766d4bdf8e815c0...1b603096cf70b04784a5d6d76cf7f738c03d0875
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[med-svn] [Git][med-team/toil][master] 4 commits: remove recommend on "python3-futures"
Michael R. Crusoe pushed to branch master at Debian Med / toil
Commits:
1eb0fb2b by Michael R. Crusoe at 2019-01-14T07:24:15Z
remove recommend on python3-futures
and depends on pytest*
- - - - -
76d73969 by Michael R. Crusoe at 2019-01-14T07:24:40Z
Refined the package description, added Provides: cwl-runner
- - - - -
c4eed1cc by Michael R. Crusoe at 2019-01-14T07:24:42Z
Use Debians newer python3-{psutil,protobuf}
But disable the mesos helper until python3-mesos is packaged
- - - - -
4028fdb2 by Michael R. Crusoe at 2019-01-14T07:25:28Z
Upload to unstable.
- - - - -
6 changed files:
- debian/changelog
- debian/control
- debian/patches/series
- + debian/patches/soften-mesos-deps
- + debian/patches/soften-pytest-depends
- debian/rules
Changes:
=
debian/changelog
=
@@ -1,3 +1,12 @@
+toil (3.18.0-2) unstable; urgency=medium
+
+ * Remove errant recommend on python3-futures and depends on python3-pytest*
+(Closes: #919228)
+ * Refined the package description, added 'Provides: cwl-runner'
+ * Remove the partial mesos support until python3-mesos is packaged
+
+ -- Michael R. Crusoe Sun, 13 Jan 2019 23:25:16
-0800
+
toil (3.18.0-1) unstable; urgency=medium
* Initial release (Closes: #851365)
=
debian/control
=
@@ -24,20 +24,24 @@ Vcs-Browser: https://salsa.debian.org/med-team/toil
Package: toil
Architecture: all
+Provides: cwl-runner
Depends: ${python3:Depends}, ${misc:Depends},
cwltool
Recommends:
python3-boto, python3-boto3,
- python3-protobuf,
- python3-futures,
+# for google cloud support
python3-libcloud
+# for mesos support, but needs python3-mesos first
+# python3-protobuf,
Suggests: python3-azure, python3-azure-storage
#Suggests: python-toil-doc
Description: cross-platform workflow engine
Toil is a scalable, efficient, cross-platform and easy-to-use workflow
engine in pure Python. It works with several well established load
- balancers like Slurm or the Sun Grid Engine. Toil is compatible with
- the Common Workflow Language (CWL).
+ balancers like Slurm or the Sun Grid Engine. Toil is also compatible with
+ the Common Workflow Language (CWL) via the "toil-cwl-runner" interface, which
+ this package make available via the Debian alternativess system under the
+ alias "cwl-runner".
#Package: python-toil-doc
#Architecture: all
=
debian/patches/series
=
@@ -6,3 +6,5 @@ debianize_docs
spelling
adjust_to_newer_cwltool
fix_tests
+soften-pytest-depends
+soften-mesos-deps
=
debian/patches/soften-mesos-deps
=
@@ -0,0 +1,15 @@
+Author: Michael R. Crusoe
+Subject: Use Debian's newer python3-psutil
+--- toil.orig/setup.py
toil/setup.py
+@@ -24,8 +24,8 @@
+ boto3 = 'boto3>=1.7.50, <2.0'
+ futures = 'futures==3.1.1'
+ pycryptodome = 'pycryptodome==3.5.1'
+-psutil = 'psutil==3.0.1'
+-protobuf = 'protobuf==3.5.1'
++psutil = 'psutil>=3.0.1'
++protobuf = 'protobuf>=3.5.1'
+ azureCosmosdbTable = 'azure-cosmosdb-table==0.37.1'
+ azureAnsible = 'ansible[azure]==2.5.0a1'
+ azureStorage = 'azure-storage==0.35.1'
=
debian/patches/soften-pytest-depends
=
@@ -0,0 +1,24 @@
+Author: Michael R. Crusoe
+Description: No need to depend on testing libraries
+--- toil.orig/setup.py
toil/setup.py
+@@ -45,8 +45,6 @@
+ docker = 'docker==2.5.1'
+ subprocess32 = 'subprocess32<=3.5.2'
+ dateutil = 'python-dateutil'
+-pytest = 'pytest==3.7.4'
+-pytest_cov = 'pytest-cov==2.5.1'
+
+ core_reqs = [
+ dill,
+@@ -56,9 +54,7 @@
+ docker,
+ dateutil,
+ psutil,
+-subprocess32,
+-pytest,
+-pytest_cov]
++subprocess32]
+
+ mesos_reqs = [
+ psutil,
=
debian/rules
=
@@ -18,6 +18,8 @@ override_dh_auto_build:
override_dh_auto_install:
dh_auto_install
find $(CURDIR)/debian -name cwltoil -delete
+ # remove the below once mesos is packaged and tested
+ find $(CURDIR)/debian -name _toil_mesos_executor -delete
# more py3 test fixes need to be cherry-picked from upstream
# override_dh_auto_test:
View it on GitLab:
https://salsa.debian.org/med-team/toil/compare/380667a975bdc247cfd5c10ed600717052885e81...4028fdb2d11226d478e7296db766d4bdf8e815c0
--
View it on GitLab:
https://salsa.debian.org/med-team/toil/compare/380667a975bdc247cfd5c10ed600717052885e81...4028fdb2d11226d478e7296db766d4bdf8e815c0
You're receiving this email because of your account on salsa.debian.org.
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[med-svn] [Git][med-team/toil] Pushed new tag debian/3.18.0-2
Michael R. Crusoe pushed new tag debian/3.18.0-2 at Debian Med / toil -- View it on GitLab: https://salsa.debian.org/med-team/toil/tree/debian/3.18.0-2 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/toil] Pushed new tag debian/3.18.0-1
Michael R. Crusoe pushed new tag debian/3.18.0-1 at Debian Med / toil -- View it on GitLab: https://salsa.debian.org/med-team/toil/tree/debian/3.18.0-1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/community/helper-scripts][master] allow running on existing repos that weren't fully setup
Michael R. Crusoe pushed to branch master at Debian Med / community /
helper-scripts
Commits:
85d1b05d by Michael R. Crusoe at 2019-01-14T09:34:25Z
allow running on existing repos that werent fully setup
- - - - -
1 changed file:
- inject-into-salsa-git
Changes:
=
inject-into-salsa-git
=
@@ -36,17 +36,32 @@ if [ "$SALSA_GROUP_ID" = "" ] ; then
exit 1
fi
+# Did we already push to salsa?
set -x
-RESPONSE=$(curl "$SALSA_URL/projects?private_token=$SALSA_TOKEN" \
- --data
"path=${DEBPKGNAME}_id=${SALSA_GROUP_ID}=${SHORTDESC}=public")
+RESPONSE=$(curl "$SALSA_URL/projects?search=${DEBPKGNAME}")
+echo $RESPONSE | jq --exit-status "map(select(.path == \"${DEBPKGNAME}\")) |
.[0].id" > /dev/null
+set +x
+if [ $? -ne 0 ]; then
+# Seems like not, lets create a project
+set -x
+RESPONSE=$(curl "$SALSA_URL/projects?private_token=$SALSA_TOKEN" \
+--data
"path=${DEBPKGNAME}_id=${SALSA_GROUP_ID}=${SHORTDESC}=public")
-echo $RESPONSE | jq --exit-status .id > /dev/null
-check_return_code
+echo $RESPONSE | jq --exit-status .id > /dev/null
+check_return_code
-PROJECT_ID=$(echo $RESPONSE | jq '.id')
-set +x
+PROJECT_ID=$(echo $RESPONSE | jq '.id')
+set +x
+else
+set -x
+PROJECT_ID=$(echo $RESPONSE | jq "map(select(.path == \"${DEBPKGNAME}\"))
| .[0].id")
+set +x
+fi
-git remote add origin g...@salsa.debian.org:${SALSA_GROUP}/${DEBPKGNAME}.git
+git remote show origin
+if [ $? -ne 0 ] ; then
+git remote add origin
g...@salsa.debian.org:${SALSA_GROUP}/${DEBPKGNAME}.git
+fi
git push origin master
git push --all --set-upstream
git push --tags
View it on GitLab:
https://salsa.debian.org/med-team/community/helper-scripts/commit/85d1b05d244bb2eaab0a050eb1bbb3039cffd352
--
View it on GitLab:
https://salsa.debian.org/med-team/community/helper-scripts/commit/85d1b05d244bb2eaab0a050eb1bbb3039cffd352
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[med-svn] [Git][med-team/toil][master] basic smoke test
Michael R. Crusoe pushed to branch master at Debian Med / toil Commits: 9e206f96 by Michael R. Crusoe at 2019-01-14T09:59:43Z basic smoke test - - - - - 3 changed files: - debian/changelog - + debian/tests/control - + debian/tests/smoke-test Changes: = debian/changelog = @@ -1,3 +1,9 @@ +toil (3.18.0-3) UNRELEASED; urgency=medium + + * Add basic smoke test ( `toil* --help` ) as an AutoPkgTest + + -- Michael R. Crusoe Mon, 14 Jan 2019 01:52:44 -0800 + toil (3.18.0-2) unstable; urgency=medium * Remove errant recommend on python3-futures and depends on python3-pytest* = debian/tests/control = @@ -0,0 +1,2 @@ +Tests: smoke-test +Depends: toil = debian/tests/smoke-test = @@ -0,0 +1,4 @@ +#!/bin/sh -e +toil --help +toil-cwl-runner --help +toil-wdl-runner --help View it on GitLab: https://salsa.debian.org/med-team/toil/commit/9e206f96af469d30d07fd517cc1f63febd17bc16 -- View it on GitLab: https://salsa.debian.org/med-team/toil/commit/9e206f96af469d30d07fd517cc1f63febd17bc16 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/cwltool][master] testing with Docker doesn't work; add curl
Michael R. Crusoe pushed to branch master at Debian Med / cwltool Commits: ea9cdf62 by Michael R. Crusoe at 2018-12-31T06:48:12Z testing with Docker doesnt work; add curl - - - - - 2 changed files: - debian/changelog - debian/tests/control Changes: = debian/changelog = @@ -1,3 +1,9 @@ +cwltool (1.0.20181217162649+dfsg-6) unstable; urgency=medium + + * debian/tests/control: testing with Docker doesn't work; add curl + + -- Michael R. Crusoe Sun, 30 Dec 2018 22:48:06 -0800 + cwltool (1.0.20181217162649+dfsg-5) unstable; urgency=medium * debian/tests/control: needed python3-pytest-mock, not python3-mock = debian/tests/control = @@ -1,3 +1,3 @@ Tests: run-tests -Depends: @, python3-pytest-xdist, python3-pytest-mock, python3-pytest-runner, nodejs, singularity-container, docker.io +Depends: @, python3-pytest-xdist, python3-pytest-mock, python3-pytest-runner, nodejs, singularity-container, curl Restrictions: allow-stderr View it on GitLab: https://salsa.debian.org/med-team/cwltool/commit/ea9cdf6229fb6ff1d170b3b8f4f29744fcae5552 -- View it on GitLab: https://salsa.debian.org/med-team/cwltool/commit/ea9cdf6229fb6ff1d170b3b8f4f29744fcae5552 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/cwltool] Pushed new tag debian/1.0.20181217162649+dfsg-6
Michael R. Crusoe pushed new tag debian/1.0.20181217162649+dfsg-6 at Debian Med / cwltool -- View it on GitLab: https://salsa.debian.org/med-team/cwltool/tree/debian/1.0.20181217162649+dfsg-6 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/khmer] Pushed new tag debian/2.1.2+dfsg-6
Michael R. Crusoe pushed new tag debian/2.1.2+dfsg-6 at Debian Med / khmer -- View it on GitLab: https://salsa.debian.org/med-team/khmer/tree/debian/2.1.2+dfsg-6 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/khmer][master] Fix building arch-independent packages separately.
Michael R. Crusoe pushed to branch master at Debian Med / khmer
Commits:
88f5bd72 by Michael R. Crusoe at 2019-01-09T15:27:54Z
Fix building arch-independent packages separately.
- - - - -
3 changed files:
- debian/changelog
- debian/control
- debian/rules
Changes:
=
debian/changelog
=
@@ -1,3 +1,9 @@
+khmer (2.1.2+dfsg-6) unstable; urgency=medium
+
+ * Fix building arch-independent packages separately.
+
+ -- Michael R. Crusoe Wed, 09 Jan 2019 07:27:45
-0800
+
khmer (2.1.2+dfsg-5) unstable; urgency=medium
* Fix liboxli-dev autopkgtest.
=
debian/control
=
@@ -30,6 +30,7 @@ Homepage: http://khmer.readthedocs.org
Package: khmer-common
Architecture: all
Multi-Arch: foreign
+Built-Using: ${sphinxdoc:Built-Using}
Depends: file,
${misc:Depends},
${sphinxdoc:Depends},
=
debian/rules
=
@@ -47,6 +47,7 @@ override_dh_sphinxdoc:
rdfind -makesymlinks true -followsymlinks true\
/usr/lib/python3/dist-packages/guzzle_sphinx_theme \
$(shell find debian/khmer-common | grep -i -v citation)
- rm
debian/khmer-common/usr/share/doc/khmer-common/html/_sources/citations.rst.txt
- cd debian/khmer-common/usr/share/doc/khmer-common/html/_sources/ && \
- ln -s ../../CITATION citations.rst.txt
+ if [ -f
debian/khmer-common/usr/share/doc/khmer-common/html/_sources/citations.rst.txt
]; then \
+ rm
debian/khmer-common/usr/share/doc/khmer-common/html/_sources/citations.rst.txt
&& \
+ cd debian/khmer-common/usr/share/doc/khmer-common/html/_sources/ && \
+ ln -s ../../CITATION citations.rst.txt; fi
View it on GitLab:
https://salsa.debian.org/med-team/khmer/commit/88f5bd72ccedb50ba5071089395fe5ac4868d0e1
--
View it on GitLab:
https://salsa.debian.org/med-team/khmer/commit/88f5bd72ccedb50ba5071089395fe5ac4868d0e1
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[med-svn] [Git][med-team/mypy][upstream] New upstream version 0.620
Michael R. Crusoe pushed to branch upstream at Debian Med / mypy Commits: 09c25437 by Michael R. Crusoe at 2018-08-07T17:58:48Z New upstream version 0.620 - - - - - 19 changed files: - MANIFEST.in - PKG-INFO - README.md - docs/source/additional_features.rst - docs/source/cheat_sheet_py3.rst - docs/source/command_line.rst - docs/source/config_file.rst - docs/source/index.rst - docs/source/installed_packages.rst - docs/source/more_types.rst - docs/source/revision_history.rst - extensions/mypy_extensions.py - extensions/setup.py - mypy.egg-info/PKG-INFO - mypy.egg-info/SOURCES.txt - mypy/applytype.py - mypy/binder.py - mypy/build.py - mypy/checker.py The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/mypy/commit/09c25437849e9f651fb0122059604cf426c45d0e -- View it on GitLab: https://salsa.debian.org/med-team/mypy/commit/09c25437849e9f651fb0122059604cf426c45d0e You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/mypy] Pushed new tag upstream/0.620
Michael R. Crusoe pushed new tag upstream/0.620 at Debian Med / mypy -- View it on GitLab: https://salsa.debian.org/med-team/mypy/tree/upstream/0.620 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/mypy][master] 3 commits: New upstream version 0.620
Michael R. Crusoe pushed to branch master at Debian Med / mypy Commits: 09c25437 by Michael R. Crusoe at 2018-08-07T17:58:48Z New upstream version 0.620 - - - - - 0508a171 by Michael R. Crusoe at 2018-08-07T17:58:58Z Update upstream source from tag upstream/0.620 Update to upstream version 0.620 with Debian dir 409a197b401739ae079d9ab4f1d7a98c7b0468c2 - - - - - fc7a3f68 by Michael R. Crusoe at 2018-08-07T18:09:17Z 0.620-1 - - - - - 22 changed files: - MANIFEST.in - PKG-INFO - README.md - debian/changelog - debian/control - debian/rules - docs/source/additional_features.rst - docs/source/cheat_sheet_py3.rst - docs/source/command_line.rst - docs/source/config_file.rst - docs/source/index.rst - docs/source/installed_packages.rst - docs/source/more_types.rst - docs/source/revision_history.rst - extensions/mypy_extensions.py - extensions/setup.py - mypy.egg-info/PKG-INFO - mypy.egg-info/SOURCES.txt - mypy/applytype.py - mypy/binder.py - mypy/build.py - mypy/checker.py The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/mypy/compare/fbfd9f47264a2a57082274d201a50c2a54f8d656...fc7a3f68631f86ef07dc7964aabf0f09d6e20f6f -- View it on GitLab: https://salsa.debian.org/med-team/mypy/compare/fbfd9f47264a2a57082274d201a50c2a54f8d656...fc7a3f68631f86ef07dc7964aabf0f09d6e20f6f You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/mypy][pristine-tar] pristine-tar data for mypy_0.620.orig.tar.gz
Michael R. Crusoe pushed to branch pristine-tar at Debian Med / mypy Commits: 0369bc2b by Michael R. Crusoe at 2018-08-07T17:58:58Z pristine-tar data for mypy_0.620.orig.tar.gz - - - - - 2 changed files: - + mypy_0.620.orig.tar.gz.delta - + mypy_0.620.orig.tar.gz.id Changes: = mypy_0.620.orig.tar.gz.delta = Binary files /dev/null and b/mypy_0.620.orig.tar.gz.delta differ = mypy_0.620.orig.tar.gz.id = @@ -0,0 +1 @@ +890cce30157a2b46e7399e1502e1911f0eb9ca55 View it on GitLab: https://salsa.debian.org/med-team/mypy/commit/0369bc2b73b35956f91e299b44283b5af42a8aab -- View it on GitLab: https://salsa.debian.org/med-team/mypy/commit/0369bc2b73b35956f91e299b44283b5af42a8aab You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/mypy] Pushed new tag debian/0.620-1
Michael R. Crusoe pushed new tag debian/0.620-1 at Debian Med / mypy -- View it on GitLab: https://salsa.debian.org/med-team/mypy/tree/debian/0.620-1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/mypy][pristine-tar] pristine-tar data for mypy_0.630.orig.tar.gz
Michael R. Crusoe pushed to branch pristine-tar at Debian Med / mypy Commits: 1be18588 by Michael R. Crusoe at 2018-09-17T16:32:52Z pristine-tar data for mypy_0.630.orig.tar.gz - - - - - 2 changed files: - + mypy_0.630.orig.tar.gz.delta - + mypy_0.630.orig.tar.gz.id Changes: = mypy_0.630.orig.tar.gz.delta = Binary files /dev/null and b/mypy_0.630.orig.tar.gz.delta differ = mypy_0.630.orig.tar.gz.id = @@ -0,0 +1 @@ +2a4c51e1e70d8e771cc282d94029b5a535f33963 View it on GitLab: https://salsa.debian.org/med-team/mypy/commit/1be18588ebf446d2da14f66e3495854f2cc808b8 -- View it on GitLab: https://salsa.debian.org/med-team/mypy/commit/1be18588ebf446d2da14f66e3495854f2cc808b8 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/mypy][upstream] New upstream version 0.630
Michael R. Crusoe pushed to branch upstream at Debian Med / mypy Commits: d0b03406 by Michael R. Crusoe at 2018-09-17T16:32:30Z New upstream version 0.630 - - - - - 30 changed files: - MANIFEST.in - PKG-INFO - + docs/.DS_Store - + docs/build/.DS_Store - + docs/build/doctrees/additional_features.doctree - + docs/build/doctrees/builtin_types.doctree - + docs/build/doctrees/casts.doctree - + docs/build/doctrees/cheat_sheet.doctree - + docs/build/doctrees/cheat_sheet_py3.doctree - + docs/build/doctrees/class_basics.doctree - + docs/build/doctrees/command_line.doctree - + docs/build/doctrees/common_issues.doctree - + docs/build/doctrees/config_file.doctree - + docs/build/doctrees/duck_type_compatibility.doctree - + docs/build/doctrees/dynamic_typing.doctree - + docs/build/doctrees/environment.pickle - + docs/build/doctrees/existing_code.doctree - + docs/build/doctrees/extending_mypy.doctree - + docs/build/doctrees/faq.doctree - + docs/build/doctrees/generics.doctree - + docs/build/doctrees/getting_started.doctree - + docs/build/doctrees/index.doctree - + docs/build/doctrees/installed_packages.doctree - + docs/build/doctrees/introduction.doctree - + docs/build/doctrees/kinds_of_types.doctree - + docs/build/doctrees/metaclasses.doctree - + docs/build/doctrees/more_types.doctree - + docs/build/doctrees/mypy_daemon.doctree - + docs/build/doctrees/protocols.doctree - + docs/build/doctrees/python2.doctree The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/mypy/commit/d0b034061cf7ed30bc8244794d930ebbf51f1b38 -- View it on GitLab: https://salsa.debian.org/med-team/mypy/commit/d0b034061cf7ed30bc8244794d930ebbf51f1b38 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/mypy][master] 3 commits: New upstream version 0.630
Michael R. Crusoe pushed to branch master at Debian Med / mypy Commits: d0b03406 by Michael R. Crusoe at 2018-09-17T16:32:30Z New upstream version 0.630 - - - - - 8109b8cc by Michael R. Crusoe at 2018-09-17T16:32:52Z Update upstream source from tag upstream/0.630 Update to upstream version 0.630 with Debian dir fac8a6e0c00a619352a7e39db892f4809501f666 - - - - - e60248d7 by Michael R. Crusoe at 2018-09-17T18:07:25Z 0.630-1 - - - - - 30 changed files: - MANIFEST.in - PKG-INFO - debian/changelog - debian/control - debian/patches/adjust-test-py-path - debian/rules - + docs/.DS_Store - + docs/build/.DS_Store - + docs/build/doctrees/additional_features.doctree - + docs/build/doctrees/builtin_types.doctree - + docs/build/doctrees/casts.doctree - + docs/build/doctrees/cheat_sheet.doctree - + docs/build/doctrees/cheat_sheet_py3.doctree - + docs/build/doctrees/class_basics.doctree - + docs/build/doctrees/command_line.doctree - + docs/build/doctrees/common_issues.doctree - + docs/build/doctrees/config_file.doctree - + docs/build/doctrees/duck_type_compatibility.doctree - + docs/build/doctrees/dynamic_typing.doctree - + docs/build/doctrees/environment.pickle - + docs/build/doctrees/existing_code.doctree - + docs/build/doctrees/extending_mypy.doctree - + docs/build/doctrees/faq.doctree - + docs/build/doctrees/generics.doctree - + docs/build/doctrees/getting_started.doctree - + docs/build/doctrees/index.doctree - + docs/build/doctrees/installed_packages.doctree - + docs/build/doctrees/introduction.doctree - + docs/build/doctrees/kinds_of_types.doctree - + docs/build/doctrees/metaclasses.doctree The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/mypy/compare/fc7a3f68631f86ef07dc7964aabf0f09d6e20f6f...e60248d73ebfd08f89ff0e4ecc382ea881cd4ff9 -- View it on GitLab: https://salsa.debian.org/med-team/mypy/compare/fc7a3f68631f86ef07dc7964aabf0f09d6e20f6f...e60248d73ebfd08f89ff0e4ecc382ea881cd4ff9 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/mypy] Pushed new tag upstream/0.630
Michael R. Crusoe pushed new tag upstream/0.630 at Debian Med / mypy -- View it on GitLab: https://salsa.debian.org/med-team/mypy/tree/upstream/0.630 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/mypy] Pushed new tag debian/0.630-1
Michael R. Crusoe pushed new tag debian/0.630-1 at Debian Med / mypy -- View it on GitLab: https://salsa.debian.org/med-team/mypy/tree/debian/0.630-1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/community/package_template][master] skip preleases on GitHub
Michael R. Crusoe pushed to branch master at Debian Med / community / package_template Commits: 31394ee9 by Michael R. Crusoe at 2018-12-19T09:50:19Z skip preleases on GitHub - - - - - 1 changed file: - debian/watch Changes: = debian/watch = @@ -18,7 +18,7 @@ version=4 # Uncomment to find new files on Github # - when using releases: -# https://github.com/#GITHUBUSER#/#PACKAGE#/releases .*/archive/#PREFIX#@ANY_VERSION@@ARCHIVE_EXT@ +# https://github.com/#GITHUBUSER#/#PACKAGE#/releases/latest .*/archive/#PREFIX#@ANY_VERSION@@ARCHIVE_EXT@ # - when using tags # https://github.com/#GITHUBUSER#/#PACKAGE#/tags .*/#PREFIX#@ANY_VERSION@@ARCHIVE_EXT@ # Remark: frequently you can do s/#PREFIX#/v?/ since 'v' or nothing is quite common but there are other prefixes possible View it on GitLab: https://salsa.debian.org/med-team/community/package_template/commit/31394ee910231c9bc2b298a0ebe52943c57e6e4e -- View it on GitLab: https://salsa.debian.org/med-team/community/package_template/commit/31394ee910231c9bc2b298a0ebe52943c57e6e4e You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/htslib][master] 3 commits: Try dropping to gcc-7 on i386*
Michael R. Crusoe pushed to branch master at Debian Med / htslib
Commits:
103be525 by Michael R. Crusoe at 2018-12-11T02:13:22Z
Try dropping to gcc-7 on i386*
- - - - -
c6579182 by Michael R. Crusoe at 2018-12-18T08:38:50Z
try suggestion from
https://github.com/samtools/htslib/issues/565#issuecomment-448028771
- - - - -
112a679b by Michael R. Crusoe at 2018-12-19T15:30:39Z
Bring i386 build enhancements to unstable.
- - - - -
4 changed files:
- debian/changelog
- debian/control
- + debian/htslib-test.lintian-overrides
- debian/rules
Changes:
=
debian/changelog
=
@@ -1,3 +1,22 @@
+htslib (1.9-7) unstable; urgency=medium
+
+ * Bring i386 build enhancements to unstable.
+
+ -- Michael R. Crusoe Wed, 19 Dec 2018 07:30:24
-0800
+
+htslib (1.9-7~1~i386~1) experimental; urgency=medium
+
+ * Turn on SSE for i386, as suggested at
+https://github.com/samtools/htslib/issues/565#issuecomment-448028771
+
+ -- Michael R. Crusoe Tue, 18 Dec 2018 00:27:40
-0800
+
+htslib (1.9-7~0~i386~gcc7~1) experimental; urgency=medium
+
+ * Try dropping to gcc-7 on i386*
+
+ -- Michael R. Crusoe Mon, 10 Dec 2018 18:02:16
-0800
+
htslib (1.9-6) unstable; urgency=medium
* Revert libdeflate for DEFLATE based (de)compression and its crc32
=
debian/control
=
@@ -18,7 +18,7 @@ Vcs-Git: https://salsa.debian.org/med-team/htslib.git
Homepage: https://github.com/samtools/htslib
Package: libhts2
-Architecture: amd64 arm64 armel armhf mips mips64el mipsel ppc64el s390x alpha
hppa ia64 kfreebsd-amd64 m68k powerpc powerpcspe ppc64 riscv64 sh4 sparc64 x32
+Architecture: any
Multi-Arch: same
Section: libs
Depends: ${misc:Depends},
@@ -37,7 +37,7 @@ Description: C library for high-throughput sequencing data
formats
new index and then for the old if the new index is absent.
Package: libhts-dev
-Architecture: amd64 arm64 armel armhf mips mips64el mipsel ppc64el s390x alpha
hppa ia64 kfreebsd-amd64 m68k powerpc powerpcspe ppc64 riscv64 sh4 sparc64 x32
+Architecture: any
Multi-Arch: same
Section: libdevel
Depends: libhts2 (= ${binary:Version}),
@@ -97,7 +97,7 @@ Description: Test data for HTSlib
This package contains test files and scripts for the HTSlib.
Package: tabix
-Architecture: amd64 arm64 armel armhf mips mips64el mipsel ppc64el s390x alpha
hppa ia64 kfreebsd-amd64 m68k powerpc powerpcspe ppc64 riscv64 sh4 sparc64 x32
+Architecture: any
Depends: ${misc:Depends},
${shlibs:Depends}
Description: generic indexer for TAB-delimited genome position files
=
debian/htslib-test.lintian-overrides
=
@@ -0,0 +1,2 @@
+# As needed for testing
+duplicated-compressed-file usr/share/htslib-test/test/bgziptest.txt.gz
=
debian/rules
=
@@ -8,9 +8,9 @@ export DH_VERBOSE=1
include /usr/share/dpkg/default.mk
ifneq (,$(filter $(DEB_HOST_ARCH),i386 kfreebsd-i386 hurd-i386))
- export DEB_CFLAGS_MAINT_APPEND=-fno-strict-aliasing -fno-code-hoisting
+ DEB_CFLAGS_MAINT_APPEND=-msse -mfpmath=sse
endif
-DEB_CFLAGS_MAINT_APPEND+=-flto
+export DEB_CFLAGS_MAINT_APPEND+=-flto
export DEB_LDFLAGS_MAINT_APPEND+=-Wl,-flto
%:
View it on GitLab:
https://salsa.debian.org/med-team/htslib/compare/147dd8065ebf3de7d68827ce34b14c84f5904bad...112a679b765dda2f1904b3d948203c9786239c1f
--
View it on GitLab:
https://salsa.debian.org/med-team/htslib/compare/147dd8065ebf3de7d68827ce34b14c84f5904bad...112a679b765dda2f1904b3d948203c9786239c1f
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[med-svn] [Git][med-team/htslib] Pushed new tag debian/1.9-7
Michael R. Crusoe pushed new tag debian/1.9-7 at Debian Med / htslib -- View it on GitLab: https://salsa.debian.org/med-team/htslib/tree/debian/1.9-7 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/mypy][master] Upload to unstable
Michael R. Crusoe pushed to branch master at Debian Med / mypy Commits: 63bce9c8 by Andreas Tille at 2019-01-24T23:05:31Z Upload to unstable - - - - - 2 changed files: - debian/changelog - debian/tests/control Changes: = debian/changelog = @@ -1,3 +1,9 @@ +mypy (0.660-4) unstable; urgency=medium + + * Fix the autopkgtests. Closes: #920048 + + -- Michael R. Crusoe Thu, 24 Jan 2019 14:56:34 -0800 + mypy (0.660-3) unstable; urgency=medium * Team upload. = debian/tests/control = @@ -1,3 +1,3 @@ Tests: run-unit-test Depends: mypy, python3-pytest-xdist, python3-virtualenv - +Restrictions: allow-stderr View it on GitLab: https://salsa.debian.org/med-team/mypy/commit/63bce9c830033eba134179bc24e904ef92e001d5 -- View it on GitLab: https://salsa.debian.org/med-team/mypy/commit/63bce9c830033eba134179bc24e904ef92e001d5 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/mypy] Pushed new tag debian/0.660-4
Michael R. Crusoe pushed new tag debian/0.660-4 at Debian Med / mypy -- View it on GitLab: https://salsa.debian.org/med-team/mypy/tree/debian/0.660-4 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/toil][master] Make the build reproducible
Michael R. Crusoe pushed to branch master at Debian Med / toil
Commits:
79a1d34d by Michael R. Crusoe at 2019-03-21T02:48:15Z
Make the build reproducible
- - - - -
3 changed files:
- debian/changelog
- + debian/patches/reproducible-build.patch
- debian/patches/series
Changes:
=
debian/changelog
=
@@ -1,3 +1,10 @@
+toil (3.18.0-3) UNRELEASED; urgency=medium
+
+ * Make the build reproducible, patch from la...@debian.org; thanks!
+(Closes: #925191)
+
+ -- Michael R. Crusoe Wed, 20 Mar 2019 21:46:34
-0500
+
toil (3.18.0-2) unstable; urgency=medium
* Remove errant recommend on python3-futures and depends on python3-pytest*
=
debian/patches/reproducible-build.patch
=
@@ -0,0 +1,24 @@
+Subject: Make the build reproducible
+From: Chris Lamb
+Forwarded: https://github.com/DataBiosphere/toil/pull/2562
+
+--- toil-3.18.0.orig/docs/conf.py
toil-3.18.0/docs/conf.py
+@@ -18,6 +18,7 @@ import inspect
+ import re
+ from datetime import datetime
+ import toil.version
++import time
+
+ # This makes the modules located in docs/vendor/sphinxcontrib available to
import
+ sphinxPath = os.path.abspath(os.path.join(os.path.pardir,
os.path.dirname('docs/vendor/sphinxcontrib/')))
+@@ -100,7 +101,8 @@ master_doc = 'index'
+
+ # General information about the project.
+ project = u'Toil'
+-copyright = u'2015 – %i UCSC Computational Genomics Lab' % datetime.now().year
++build_date =
datetime.utcfromtimestamp(int(os.environ.get('SOURCE_DATE_EPOCH', time.time(
++copyright = u'2015 – %i UCSC Computational Genomics Lab' % build_date.year
+ author = u'UCSC Computational Genomics Lab'
+
+ # The version info for the project you're documenting, acts as replacement for
=
debian/patches/series
=
@@ -8,3 +8,4 @@ adjust_to_newer_cwltool
fix_tests
soften-pytest-depends
soften-mesos-deps
+reproducible-build.patch
View it on GitLab:
https://salsa.debian.org/med-team/toil/commit/79a1d34d23af4a39a8bbfeab97b20978dff45134
--
View it on GitLab:
https://salsa.debian.org/med-team/toil/commit/79a1d34d23af4a39a8bbfeab97b20978dff45134
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[med-svn] [Git][med-team/hhsuite][master] 7 commits: Upstream no longer includes the PDF in their tarball
Michael R. Crusoe pushed to branch master at Debian Med / hhsuite Commits: 4568edbb by Michael R. Crusoe at 2019-02-28T14:15:23Z Upstream no longer includes the PDF in their tarball - - - - - bc1068e5 by Michael R. Crusoe at 2019-02-28T14:16:20Z New upstream version 3.1.0 - - - - - 154c0b4d by Michael R. Crusoe at 2019-02-28T14:16:34Z Merge tag upstream/3.1.0 Upstream version 3.1.0 - - - - - f7fdfab1 by Michael R. Crusoe at 2019-02-28T14:17:16Z new upstream release. - - - - - 3de79ef3 by Michael R. Crusoe at 2019-02-28T14:45:08Z refresh patched; drop -doc package - - - - - 190f1b9d by Michael R. Crusoe at 2019-02-28T18:48:13Z ffindex needs -include stdlib.h ? - - - - - f2534c7c by Michael R. Crusoe at 2019-02-28T18:56:21Z README→README.md - - - - - 30 changed files: - .github/ISSUE_TEMPLATE.md - − .gitmodules - .travis.yml - − CHANGES - CMakeLists.txt - + Dockerfile - LICENSE - − README - README.md - + cmake/ResourceCompiler.cmake - + cmake/xxdi.pl - data/CMakeLists.txt - + data/test.sh - debian/changelog - debian/control - debian/copyright - − debian/docs - − debian/hhsuite-doc.doc-base - − debian/hhsuite-doc.docs - debian/hhsuite.docs - debian/patches/disable-AVX-SSE.patch - debian/patches/disable-ffindex-build.patch - debian/patches/drop-fmemopen.h.patch - debian/patches/perlscript_uselib - debian/patches/series - debian/rules - debian/watch - − doc/CMakeLists.txt - − doc/UseLATEX.cmake - − doc/hhblits-hhsearch.png The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/hhsuite/compare/41f888e51abe534065eb3df720469bdbf6269343...f2534c7c71ae2aebb67a2aaf660abacbd49bed60 -- View it on GitLab: https://salsa.debian.org/med-team/hhsuite/compare/41f888e51abe534065eb3df720469bdbf6269343...f2534c7c71ae2aebb67a2aaf660abacbd49bed60 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/hhsuite][pristine-tar] pristine-tar data for hhsuite_3.1.0.orig.tar.xz
Michael R. Crusoe pushed to branch pristine-tar at Debian Med / hhsuite Commits: c303f278 by Michael R. Crusoe at 2019-02-28T14:16:34Z pristine-tar data for hhsuite_3.1.0.orig.tar.xz - - - - - 2 changed files: - + hhsuite_3.1.0.orig.tar.xz.delta - + hhsuite_3.1.0.orig.tar.xz.id Changes: = hhsuite_3.1.0.orig.tar.xz.delta = Binary files /dev/null and b/hhsuite_3.1.0.orig.tar.xz.delta differ = hhsuite_3.1.0.orig.tar.xz.id = @@ -0,0 +1 @@ +87c333c2d726eb6ba62d6c285bbe0e65207d6799 View it on GitLab: https://salsa.debian.org/med-team/hhsuite/commit/c303f27803accc85b3d4a0d4f9ddf54756835b4e -- View it on GitLab: https://salsa.debian.org/med-team/hhsuite/commit/c303f27803accc85b3d4a0d4f9ddf54756835b4e You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/hhsuite][upstream] New upstream version 3.1.0
Michael R. Crusoe pushed to branch upstream at Debian Med / hhsuite Commits: bc1068e5 by Michael R. Crusoe at 2019-02-28T14:16:20Z New upstream version 3.1.0 - - - - - 16 changed files: - .github/ISSUE_TEMPLATE.md - − .gitmodules - .travis.yml - − CHANGES - CMakeLists.txt - + Dockerfile - LICENSE - − README - README.md - + cmake/ResourceCompiler.cmake - + cmake/xxdi.pl - data/CMakeLists.txt - + data/test.sh - − doc/CMakeLists.txt - − doc/UseLATEX.cmake - − doc/hhblits-hhsearch.png The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/hhsuite/commit/bc1068e5b4d051cbe8a57a30f608749f4b5be878 -- View it on GitLab: https://salsa.debian.org/med-team/hhsuite/commit/bc1068e5b4d051cbe8a57a30f608749f4b5be878 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/hhsuite][master] document the reason for the new release
Michael R. Crusoe pushed to branch master at Debian Med / hhsuite Commits: 4b9bf32a by Michael R. Crusoe at 2019-02-28T20:08:51Z document the reason for the new release - - - - - 1 changed file: - debian/changelog Changes: = debian/changelog = @@ -1,6 +1,10 @@ hhsuite (3.1.0-1) UNRELEASED; urgency=medium * New upstream release. +"Added hhsearch_omp, hhsearch_mpi, hhalign_omp and haling_mpi binaries + Removed non-GPLv3 compatible code + ffindex_apply_mpi will not crash anymore on systems with low amount of + virtual memory" -- Michael R. Crusoe Thu, 28 Feb 2019 08:16:48 -0600 View it on GitLab: https://salsa.debian.org/med-team/hhsuite/commit/4b9bf32a4f1f7fc5dcdf6c97a8d42d3d542c48e5 -- View it on GitLab: https://salsa.debian.org/med-team/hhsuite/commit/4b9bf32a4f1f7fc5dcdf6c97a8d42d3d542c48e5 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/epigrass][master] Start adding py3 and PyQt5 support
Michael R. Crusoe pushed to branch master at Debian Med / epigrass
Commits:
bcafc854 by Michael R. Crusoe at 2019-03-01T21:20:51Z
Start adding py3 and PyQt5 support
- - - - -
7 changed files:
- debian/changelog
- + debian/clean
- debian/control
- + debian/patches/py3
- debian/patches/series
- − debian/patches/sqlite3.patch
- debian/rules
Changes:
=
debian/changelog
=
@@ -1,5 +1,7 @@
epigrass (2.4.7-3) UNRELEASED; urgency=medium
+ * Team upload.
+
[ Steffen Moeller ]
* debian/upstream/metadata:
- yamllint cleanliness
@@ -19,6 +21,9 @@ epigrass (2.4.7-3) UNRELEASED; urgency=medium
* Trim trailing whitespace.
* Use secure copyright file specification URI.
+ [ Michael R. Crusoe ]
+ * Added py3 compatability and migrated to PyQt5
+
-- Andreas Tille Wed, 17 Oct 2018 16:20:32 +0200
epigrass (2.4.7-2) unstable; urgency=medium
=
debian/clean
=
@@ -0,0 +1 @@
+epigrass/Epigrass/epimodels.c
=
debian/control
=
@@ -6,12 +6,21 @@ Section: science
Priority: optional
Build-Depends: debhelper (>= 11~),
dh-python,
- python-dev,
- python-setuptools,
- python-virtualenv,
- python-sqlsoup,
- python-redis,
- cython
+ python3-dev,
+ python3-setuptools,
+ python3-virtualenv,
+ python3-sqlsoup,
+ python3-redis,
+ python3-requests,
+ python3-numpy,
+ python3-networkx,
+ python3-dbfread,
+ python3-mysqldb,
+ python3-matplotlib,
+ python3-gdal,
+ python3-pyqt5.qwt,
+ python3-pyqt5.qtopengl,
+ cython3
Standards-Version: 4.2.1
Vcs-Browser: https://salsa.debian.org/med-team/epigrass
Vcs-Git: https://salsa.debian.org/med-team/epigrass.git
@@ -21,21 +30,21 @@ Package: epigrass
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends},
- ${python:Depends},
- python-sqlobject,
- python-qt4-gl,
- python-qwt5-qt4,
- python-numpy,
- python-gdal,
- python-formencode,
- python-mysqldb,
- python-pysqlite2,
- python-matplotlib,
- python-networkx,
- python-pkg-resources,
- python-sqlalchemy,
- python-sqlsoup,
- python-redis,
+ ${python3:Depends},
+ python3-sqlobject,
+ python3-pyqt5.qwt,
+ python3-pyqt5.qtopengl,
+ python3-numpy,
+ python3-gdal,
+ python3-formencode,
+ python3-mysqldb,
+ python3-matplotlib,
+ python3-networkx,
+ python3-pkg-resources,
+ python3-sqlalchemy,
+ python3-sqlsoup,
+ python3-redis,
+ python3-pyglet,
redis-server
Suggests: grass,
epigrass-doc,
=
debian/patches/py3
=
The diff for this file was not included because it is too large.
=
debian/patches/series
=
@@ -1 +1 @@
-sqlite3.patch
+py3
=
debian/patches/sqlite3.patch deleted
=
@@ -1,16 +0,0 @@
-Author: V. Hiremath
-Last-Update: Wed, 21 May 2014 11:10:43 +0200
-Forwarded-Upstream: no
-Description: Use Debian packaged SQLite wrapper
-
a/Epigrass/manager.py
-+++ b/Epigrass/manager.py
-@@ -11,7 +11,7 @@ from argparse import ArgumentParser
- import ConfigParser
- import string
- import json
--import sqlite3
-+from pysqlite2 import dbapi2 as sqlite3
- import os
- import getpass
- import MySQLdb
=
debian/rules
=
@@ -6,13 +6,22 @@ export PYBUILD_DESTDIR=debian/$(DEB_SOURCE)
export DEB_BUILD_MAINT_OPTIONS = hardening=+all
%:
- dh $@ --with python2 --buildsystem=pybuild
+ dh $@ --with python3 --buildsystem=pybuild
+
+override_dh_clean:
+ dh_clean
+ rm -f Epigrass/epimodels.c
override_dh_auto_install:
dh_auto_install -- --after-install='mv
{destdir}/{install_dir}/Epigrass/egicon.png
{destdir}/usr/share/pixmaps/epigrass.png; \
ln -s
/usr/share/pixmaps/epigrass.png {destdir}/{install_dir}/Epigrass/egicon.png'
+ #PYTHONPATH=debian/epigrass/usr/lib/python3.7/dist-packages/ \
+ # debian/epigrass/usr/bin/epirunner --help
override_dh_installdocs:
# no idea why doc is installed in main package as well - just remove
this copy
dh_installdocs
rm debian/$(DEB_SOURCE)/usr/share/doc/$(DEB_SOURCE)/Epigrass.pdf*
+
+#override_dh_auto_t
[med-svn] [Git][med-team/ffindex] Pushed new tag debian/0.9.9.9-2
Michael R. Crusoe pushed new tag debian/0.9.9.9-2 at Debian Med / ffindex -- View it on GitLab: https://salsa.debian.org/med-team/ffindex/tree/debian/0.9.9.9-2 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ffindex][master] release to unstable
Michael R. Crusoe pushed to branch master at Debian Med / ffindex Commits: e961e434 by Michael R. Crusoe at 2019-03-03T19:56:50Z release to unstable - - - - - 1 changed file: - debian/changelog Changes: = debian/changelog = @@ -1,9 +1,9 @@ -ffindex (0.9.9.9-2) UNRELEASED; urgency=medium +ffindex (0.9.9.9-2) unstable; urgency=medium * Team upload. * Add patch from helmutg@ to enable cross building; thanks! Closes: #923637. - -- Michael R. Crusoe Sun, 03 Mar 2019 13:49:30 -0600 + -- Michael R. Crusoe Sun, 03 Mar 2019 13:56:41 -0600 ffindex (0.9.9.9-1) unstable; urgency=medium View it on GitLab: https://salsa.debian.org/med-team/ffindex/commit/e961e434aebd1c8800d6f8a77b2a05b5fcad6fae -- View it on GitLab: https://salsa.debian.org/med-team/ffindex/commit/e961e434aebd1c8800d6f8a77b2a05b5fcad6fae You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/hhsuite][master] 6 commits: Mark hhsuite-data as Multi-Arch: foreign
Michael R. Crusoe pushed to branch master at Debian Med / hhsuite
Commits:
d88e87c3 by Michael R. Crusoe at 2019-03-01T10:10:43Z
Mark hhsuite-data as Multi-Arch: foreign
- - - - -
2ba87486 by Michael R. Crusoe at 2019-03-01T10:17:39Z
add missing ${perl:Depends}
- - - - -
bb8d63d8 by Michael R. Crusoe at 2019-03-01T10:24:17Z
add new reference to 10.1101/560029
- - - - -
424fb601 by Michael R. Crusoe at 2019-03-01T10:53:24Z
update copyright
- - - - -
87d1893f by Michael R. Crusoe at 2019-03-01T10:53:43Z
misc
- - - - -
27e34bf7 by Michael R. Crusoe at 2019-03-01T10:55:44Z
docs are gone
- - - - -
4 changed files:
- debian/changelog
- debian/control
- debian/copyright
- debian/upstream/metadata
Changes:
=
debian/changelog
=
@@ -1,10 +1,16 @@
hhsuite (3.1.0-1) UNRELEASED; urgency=medium
+ * Team upload.
* New upstream release.
"Added hhsearch_omp, hhsearch_mpi, hhalign_omp and haling_mpi binaries
Removed non-GPLv3 compatible code
ffindex_apply_mpi will not crash anymore on systems with low amount of
virtual memory"
+ * The non-GPLv3 code was in src/hhprefilter.cpp; now gone
+ * Mark hhsuite-data as Multi-Arch: foreign
+ * Drop hhsuite-doc: documentation moved by upstream to
+https://github.com/soedinglab/hh-suite/wiki
+ * Removed '-march=native'
-- Michael R. Crusoe Thu, 28 Feb 2019 08:16:48
-0600
=
debian/control
=
@@ -8,8 +8,6 @@ Priority: optional
Build-Depends: debhelper (>= 11~),
libffindex0-dev (>= 0.9.9.8),
cmake,
- texlive-latex-base,
- texlive-latex-recommended,
imagemagick,
help2man
Standards-Version: 4.3.0
@@ -21,6 +19,7 @@ Package: hhsuite
Architecture: amd64
Depends: ${shlibs:Depends},
${misc:Depends},
+ ${perl:Depends},
ffindex (>= 0.9.9.8),
hhsuite-data (= ${source:Version}),
python
@@ -46,6 +45,7 @@ Description: sensitive protein sequence searching based on
HMM-HMM alignment
Package: hhsuite-data
Architecture: all
+Multi-Arch: foreign
Depends: ${misc:Depends}
Description: sensitive protein sequence searching based on HMM-HMM alignment
(data)
HH-suite is an open-source software package for sensitive protein sequence
=
debian/copyright
=
@@ -3,12 +3,14 @@ Upstream-Name: hhsuite
Upstream-Contact: Andreas Hauser
Johannes Soeding
Source:
ftp://toolkit.lmb.uni-muenchen.de/HH-suite/releases/hhsuite-([0-9.]+)\.tar\.gz
+File-Excluded: scripts/hhpred/
+ lib/ffindex/
Files: *
Copyright: 2006, 2012 Johannes Soeding
2012 Michael Remmert
2012 Andreas Hauser
- 2006, 2009, 2012 Andreas Biegert
+ 2006, 2009-2012 Andreas Biegert
2009-2012 Christof Angermueller
License: GPL-3.0+
@@ -16,13 +18,25 @@ Files: src/cs/getopt_pp.h src/cs/getopt_pp.cc
Copyright: 2007, 2008 Daniel Gutson, FuDePAN
License: GPL-3.0+
+Files: src/hhprefilter.h
+Copyright: 2012-2015, Boston College.
+License: Expat
+
Files: debian/*
Copyright: 2012 Laszlo Kajan
+ 2019 Michael R. Crusoe
License: GPL-3.0+
+Files: cmake/xxdi.pl
+Copyright: 2013, Linux Foundation
+ 2013, Greg Kroah-Hartman
+License: GPL-2
+
Files: cmake/FindASan.cmake cmake/FindMSan.cmake cmake/FindTSan.cmake
cmake/FindUBSan.cmake
Copyright: 2013 Matthew Arsenault
-License: MIT
+License: Expat
+
+License: Expat
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
@@ -41,15 +55,6 @@ License: MIT
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.
-Files: doc/UseLATEX.cmake
-Copyright: 2004 Sandia Corporation
-License: Sandia
- Under the terms of Contract DE-AC04-94AL85000, there is a non-exclusive
- license for use of this work by or on behalf of the
- U.S. Government. Redistribution and use in source and binary forms, with
- or without modification, are permitted provided that this Notice and any
- statement of authorship are reproduced on all copies.
-
License: GPL-3.0+
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
=
debian/upstream/metadata
=
@@ -26,6 +26,18 @@ Reference:
URL: http://bioinformatics.oxfordjournals.org/content/21/7/951.abstract
eprint: "http://bioinformatics.oxfordjournals.org/content/\
21/7/951.full.pdf+html"
+ - Author: >
+ Martin Steinegger and Markus Mei
[med-svn] [Git][med-team/ffindex][master] enable cross building
Michael R. Crusoe pushed to branch master at Debian Med / ffindex Commits: 5a7eeb53 by Michael R. Crusoe at 2019-03-03T19:51:53Z enable cross building - - - - - 4 changed files: - debian/changelog - debian/control - + debian/patches/cross.patch - debian/patches/series Changes: = debian/changelog = @@ -1,3 +1,10 @@ +ffindex (0.9.9.9-2) UNRELEASED; urgency=medium + + * Team upload. + * Add patch from helmutg@ to enable cross building; thanks! Closes: #923637. + + -- Michael R. Crusoe Sun, 03 Mar 2019 13:49:30 -0600 + ffindex (0.9.9.9-1) unstable; urgency=medium * New upstream version = debian/control = @@ -9,7 +9,8 @@ Build-Depends: debhelper (>= 12~), libopenmpi-dev, openmpi-bin, cmake (>= 3.11), - chrpath + chrpath, + pkg-config Standards-Version: 4.3.0 Vcs-Browser: https://salsa.debian.org/med-team/ffindex Vcs-Git: https://salsa.debian.org/med-team/ffindex.git = debian/patches/cross.patch = @@ -0,0 +1,42 @@ +Author: Helmut Grohne +Description: enable cross building + +ffindex fails to cross build from source, because it uses mpicc. mpicc +is unfixable in terms of cross building, which is why it is being moved +to pkg-config upstream. Rather than wrap your build in mpicc, you can +compute the relevant flags using pkg-config just like any other library. + +--- ffindex-0.9.9.9.orig/src/Makefile ffindex-0.9.9.9/src/Makefile +@@ -7,7 +7,10 @@ + #CC=gcc + #CC=icc + #CC=clang ++PKG_CONFIG?=pkg-config + CFLAGS+=-std=c99 -O2 -g -fPIC -Wall -pedantic -D_GNU_SOURCE=1 -I. $(CPPFLAGS) ++CFLAGS_MPI=$(shell $(PKG_CONFIG) --cflags mpi) ++LDFLAGS_MPI=$(shell $(PKG_CONFIG) --libs mpi) + SOCURRENT=2 + SOREVISION=0 + SOAGE=2 +@@ -61,16 +64,16 @@ + $(CC) $(CFLAGS) -o $@ ffindex_apply.o $(LDFLAGS) -L. -lffindex + + ffindex_apply_mpi: ffindex_apply_mpi.o $(FFINDEX_LIBS) +- mpicc $(CFLAGS) -DHAVE_MPI -o $@ ffindex_apply_mpi.o $(LDFLAGS) -L. -lffindex ++ $(CC) $(CFLAGS_MPI) $(LDFLAGS_MPI) $(CFLAGS) -DHAVE_MPI -o $@ ffindex_apply_mpi.o $(LDFLAGS) -L. -lffindex + + ffindex_apply_mpi.o: ffindex_apply_mpi.c $(FFINDEX_HEADERS) +- mpicc $(CFLAGS) -DHAVE_MPI -c ffindex_apply_mpi.c -o $@ ++ $(CC) $(CFLAGS_MPI) $(CFLAGS) -DHAVE_MPI -c ffindex_apply_mpi.c -o $@ + + ffindex_apply_mpi_spawn: ffindex_apply_mpi_spawn.o $(FFINDEX_LIBS) +- mpicc $(CFLAGS) -o $@ ffindex_apply_mpi_spawn.o $(LDFLAGS) ++ $(CC) $(CFLAGS_MPI) $(LDFLAGS_MPI) $(CFLAGS) -o $@ ffindex_apply_mpi_spawn.o $(LDFLAGS) + + ffindex_apply_mpi_spawn.o: ffindex_apply_mpi_spawn.o $(FFINDEX_HEADERS) +- mpicc $(CFLAGS) -c ffindex_apply_mpi_spawn.c -o $@ ++ $(CC) $(CFLAGS_MPI) $(CFLAGS) -c ffindex_apply_mpi_spawn.c -o $@ + + ffindex_from_fasta: ffindex_from_fasta.o $(FFINDEX_LIBS) + $(CC) -o $@ ffindex_from_fasta.o $(LDFLAGS) $(STATIC) = debian/patches/series = @@ -1,2 +1,3 @@ Makefile.patch basename.patch +cross.patch View it on GitLab: https://salsa.debian.org/med-team/ffindex/commit/5a7eeb53972e97ee264eb67d9df2f6c7089e4e14 -- View it on GitLab: https://salsa.debian.org/med-team/ffindex/commit/5a7eeb53972e97ee264eb67d9df2f6c7089e4e14 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/galaxy-lib][master] make autopkgtests
Michael R. Crusoe pushed to branch master at Debian Med / galaxy-lib
Commits:
74e350c7 by Michael R. Crusoe at 2019-03-10T10:35:25Z
make autopkgtests
- - - - -
5 changed files:
- + debian/README.test
- debian/docs
- + debian/examples
- + debian/tests/control
- + debian/tests/run-unit-test
Changes:
=
debian/README.test
=
@@ -0,0 +1,9 @@
+Notes on how this package can be tested.
+
+
+This package can be tested by running the provided test:
+
+sh run-unit-test
+
+in order to confirm its integrity.
+
=
debian/docs
=
@@ -1,2 +1,4 @@
README.rst
build/html
+debian/README.test
+debian/tests/run-unit-test
=
debian/examples
=
@@ -0,0 +1 @@
+tests
=
debian/tests/control
=
@@ -0,0 +1,4 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr
+
=
debian/tests/run-unit-test
=
@@ -0,0 +1,19 @@
+#!/bin/bash
+set -e
+
+pkg=python3-galaxy-lib
+
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+ AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XX)
+ # Double quote below to expand the temporary directory variable now versus
+ # later is on purpose.
+ # shellcheck disable=SC2064
+ trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+#cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
+
+#cd "${AUTOPKGTEST_TMP}"
+
+cd /usr/share/doc/${pkg}/examples
+python3 -m nose -v
View it on GitLab:
https://salsa.debian.org/med-team/galaxy-lib/commit/74e350c7d49dcfc9e46fac880265ccfd4387d40f
--
View it on GitLab:
https://salsa.debian.org/med-team/galaxy-lib/commit/74e350c7d49dcfc9e46fac880265ccfd4387d40f
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[med-svn] [Git][med-team/galaxy-lib][master] 2 commits: drop python2 package
Michael R. Crusoe pushed to branch master at Debian Med / galaxy-lib
Commits:
5fb26896 by Michael R. Crusoe at 2019-03-10T07:40:47Z
drop python2 package
- - - - -
802344d6 by Michael R. Crusoe at 2019-03-10T10:05:28Z
run tests, ship docs
- - - - -
7 changed files:
- debian/control
- + debian/doc-base
- debian/python3-galaxy-lib.docs → debian/docs
- + debian/patches/remove_badges
- + debian/patches/repro
- + debian/patches/series
- debian/rules
Changes:
=
debian/control
=
@@ -7,41 +7,30 @@ Testsuite: autopkgtest-pkg-python
Priority: optional
Build-Depends: debhelper (>= 12~),
dh-python,
- python-all,
- python-docutils,
- python-setuptools,
- python-six (>= 1.9.0),
- python-yaml,
python3-all,
python3-docutils,
python3-setuptools,
python3-six (>= 1.9.0),
- python3-yaml
+ python3-yaml,
+ python3-markupsafe,
+ python3-packaging,
+ python3-boltons,
+ python3-unittest2,
+ python3-nose,
+ python3-sphinx,
+ python3-recommonmark,
+ python3-sphinx-rtd-theme
Standards-Version: 4.3.0
Vcs-Browser: https://salsa.debian.org/med-team/galaxy-lib
Vcs-Git: https://salsa.debian.org/med-team/galaxy-lib.git
Homepage: https://github.com/galaxyproject/galaxy-lib
-Package: python-galaxy-lib
-Architecture: all
-Depends: ${misc:Depends},
- ${python:Depends}
-Recommends: ${python:Recommends}
-Suggests: ${python:Suggests}
-Description: Subset of Galaxy workflow platform's core code base - Python 2.X
- A small subset of the Galaxy project for reuse outside the core.
- The Galaxy software framework enables researchers without informatics
- expertise to perform computational analyses through the web. A user interacts
- with Galaxy through the web by uploading and analyzing the data. Galaxy
- interacts with underlying computational infrastructure (servers that run the
- analyses and disks that store the data) without exposing it to the user.
- .
- This is the Python 2.x version.
-
Package: python3-galaxy-lib
Architecture: all
Depends: ${misc:Depends},
- ${python3:Depends}
+ ${python3:Depends},
+ ${sphinxdoc:Depends}
+Built-Using: ${sphinxdoc:Built-Using}
Recommends: ${python3:Recommends}
Suggests: ${python3:Suggests}
Description: Subset of Galaxy core code base designed to be used
=
debian/doc-base
=
@@ -0,0 +1,11 @@
+Document: galaxy-lib
+Title: Galaxy-Lib Documentation
+Author: Galaxy Project and Community
+Abstract: A small subset of the Galaxy project for reuse outside the core. This
+ subset has minimal dependencies and should be Python 3 compatible.
+Section: Programming/Python
+
+Format: html
+Index: /usr/share/doc/python3-galaxy-lib/html/index.html
+Files: /usr/share/doc/python3-galaxy-lib/html/*
+
=
debian/python3-galaxy-lib.docs → debian/docs
=
@@ -1 +1,2 @@
README.rst
+build/html
=
debian/patches/remove_badges
=
@@ -0,0 +1,20 @@
+Author: Michael R. Crusoe
+Description: Respect user privacy and don't include remote images
+Forwarded: not applicable
+--- galaxy-lib.orig/README.rst
galaxy-lib/README.rst
+@@ -1,14 +1,3 @@
+-
+-.. image:: https://readthedocs.org/projects/galaxy-lib/badge/?version=latest
+- :target: http://galaxy-lib.readthedocs.io/en/latest/?badge=latest
+- :alt: Documentation Status
+-
+-.. image:: https://badge.fury.io/py/galaxy-lib.svg
+- :target: https://pypi.python.org/pypi/galaxy-lib/
+-
+-.. image:: https://travis-ci.org/galaxyproject/galaxy-lib.png?branch=master
+- :target: https://travis-ci.org/galaxyproject/galaxy-lib
+-
+ Overview
+
+
=
debian/patches/repro
=
@@ -0,0 +1,35 @@
+From: Michael R. Crusoe
+Subject: keep environment variables out of generated docs
+--- galaxy-lib.orig/galaxy/tools/verify/test_data.py
galaxy-lib/galaxy/tools/verify/test_data.py
+@@ -28,7 +28,9 @@
+
+ class TestDataResolver(object):
+
+-def __init__(self, file_dirs=None, env_var='GALAXY_TEST_FILE_DIR',
environ=os.environ):
++def __init__(self, file_dirs=None, env_var='GALAXY_TEST_FILE_DIR',
environ=None):
++if environ is None:
++environ = os.environ
+ if file_dirs is None:
+ file_dirs = environ.get(env_var, None)
+ if file_dirs is None:
+--- galaxy-lib.orig/galaxy/util/__init__.py
galaxy-lib/galaxy/util/__init__.py
+@@ -1527,7 +1527,7 @@
+ return os.path.abspath(galaxy_root_path)
+
+
+-def config_directories_fro
[med-svn] [Git][med-team/community/package_template][master] make "shellcheck clean" the run-unit-test template
Michael R. Crusoe pushed to branch master at Debian Med / community /
package_template
Commits:
5fa390ac by Michael R. Crusoe at 2019-02-17T11:07:27Z
make shellcheck clean the run-unit-test template
- - - - -
1 changed file:
- debian/tests/run-unit-test
Changes:
=
debian/tests/run-unit-test
=
@@ -3,13 +3,16 @@ set -e
pkg=#PACKAGENAME#
-if [ "$AUTOPKGTEST_TMP" = "" ] ; then
- AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XX`
- trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+ AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XX)
+ # Double quote below to expand the temporary directory variable now versus
+ # later is on purpose.
+ # shellcheck disable=SC2064
+ trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
fi
-cp -a /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP
+cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
-cd $AUTOPKGTEST_TMP
+cd "${AUTOPKGTEST_TMP}"
#do_stuff_to_test_package#
View it on GitLab:
https://salsa.debian.org/med-team/community/package_template/commit/5fa390aced1e540a585e890a4be679c955b7877a
--
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[med-svn] [Git][med-team/abyss] Pushed new tag debian/2.1.5-7
Michael R. Crusoe pushed new tag debian/2.1.5-7 at Debian Med / abyss -- View it on GitLab: https://salsa.debian.org/med-team/abyss/tree/debian/2.1.5-7 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/trinityrnaseq][master] CXXFLAGS CPPFLAGS to Chrysalis & scaffold_iworm_contigs
Michael R. Crusoe pushed to branch master at Debian Med / trinityrnaseq
Commits:
10f51f60 by Michael R. Crusoe at 2019-01-04T15:59:16Z
CXXFLAGS CPPFLAGS to Chrysalis scaffold_iworm_contigs
and add LDFALGS CPPFLAGS and unshadow CFALGS for seqtk-trinity-0.0.2
- - - - -
5 changed files:
- debian/changelog
- + debian/patches/hardening
- + debian/patches/seqtk-trinity-hardening
- debian/patches/series
- debian/rules
Changes:
=
debian/changelog
=
@@ -1,3 +1,9 @@
+trinityrnaseq (2.6.6+dfsg-7) UNRELEASED; urgency=medium
+
+ * Eliminate warning about missing hardening flags
+
+ -- Michael R. Crusoe Fri, 04 Jan 2019 07:58:22
-0800
+
trinityrnaseq (2.6.6+dfsg-6) unstable; urgency=medium
* -examples: Don't hardcode number of --CPU (especially above 2). Fixes the
=
debian/patches/hardening
=
@@ -0,0 +1,24 @@
+From: Michael R. Crusoe
+Subject: add standard CXXFLAGS CPPFLAGS to Chrysalis & scaffold_iworm_contigs
+--- trinityrnaseq.orig/Chrysalis/Makefile
trinityrnaseq/Chrysalis/Makefile
+@@ -466,7 +466,7 @@
+ # How to compile C++ files:
+ .cc.o:
+ @ mkdir -p $(OBJ)/${@D}
+- $(CPLUSPLUS) $(CPPC) -c $(SRC)/$*.cc -o $(OBJ)/$*.o
++ $(CPLUSPLUS) $(CXXFLAGS) $(CPPC) -c $(SRC)/$*.cc -o $(OBJ)/$*.o
+
+ ##
+ ## ADDITIONAL TARGETS:
+--- trinityrnaseq.orig/trinity-plugins/scaffold_iworm_contigs/Makefile
trinityrnaseq/trinity-plugins/scaffold_iworm_contigs/Makefile
+@@ -2,7 +2,7 @@
+ prefix = ../htslib
+
+ ScaffoldIwormContigs:
+- $(CXX) $(LDFLAGS) -I$(prefix) -L$(prefix) ScaffoldIwormContigs.cpp
error_checker.cpp -lhts -o scaffold_iworm_contigs
++ $(CXX) $(LDFLAGS) -I$(prefix) -L$(prefix) $(CPPFLAGS) $(CXXFLAGS)
ScaffoldIwormContigs.cpp error_checker.cpp -lhts -o scaffold_iworm_contigs
+
+ clean:
+ rm -f scaffold_iworm_contigs
=
debian/patches/seqtk-trinity-hardening
=
@@ -0,0 +1,18 @@
+From: Michael R. Crusoe
+Subject: Add LDFALGS CPPFLAGS and unshadw CFALGS for seqtk-trinity-0.0.2
+
+--- trinityrnaseq.orig/trinity-plugins/seqtk-trinity-0.0.2/Makefile
trinityrnaseq/trinity-plugins/seqtk-trinity-0.0.2/Makefile
+@@ -1,10 +1,10 @@
+ CC=gcc
+-CFLAGS=-g -Wall -O2 -Wno-unused-function
++CFLAGS+=-g -Wall -O2 -Wno-unused-function
+
+ all:seqtk-trinity
+
+ seqtk-trinity:seqtk.c khash.h kseq.h
+- $(CC) $(CFLAGS) seqtk.c -o $@ -lz -lm
++ $(CC) $(LDFLAGS) $(CPPFLAGS) $(CFLAGS) seqtk.c -o $@ -lz -lm
+
+ clean:
+ rm -fr gmon.out *.o ext/*.o a.out seqtk trimadap *~ *.a *.dSYM
session*
=
debian/patches/series
=
@@ -14,3 +14,4 @@ disable-libieee
python3
better_java_version_check
unfix_num_of_cores
+hardening
=
debian/rules
=
@@ -27,9 +27,11 @@ override_dh_auto_configure:
$(shell dpkg-buildflags --export=configure); done
override_dh_auto_build:
+ patch -p1 < debian/patches/seqtk-trinity-hardening
for target in ${SOURCE_DIRECTORIES_ALL}; do dh_auto_build \
-O--sourcedirectory=$${target}; done
+
override_dh_auto_clean:
for target in ${SOURCE_DIRECTORIES}; do dh_auto_clean \
--sourcedirectory=$${target}; done
View it on GitLab:
https://salsa.debian.org/med-team/trinityrnaseq/commit/10f51f605b9ad837d8c6cbecc1863b12519246d6
--
View it on GitLab:
https://salsa.debian.org/med-team/trinityrnaseq/commit/10f51f605b9ad837d8c6cbecc1863b12519246d6
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[med-svn] [Git][med-team/mira][master] 7 commits: update homepage URL
Michael R. Crusoe pushed to branch master at Debian Med / mira
Commits:
f1c0778d by Michael R. Crusoe at 2019-02-18T08:30:18Z
update homepage URL
- - - - -
442690a0 by Michael R. Crusoe at 2019-02-18T08:32:00Z
Mark mira-doc as Multi-Arch: foreign
- - - - -
c162cb46 by Michael R. Crusoe at 2019-02-18T08:44:59Z
Secure URI in copyright format; Standards-Version: 4.3.0
- - - - -
087de19d by Michael R. Crusoe at 2019-02-18T08:45:30Z
Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
- - - - -
dde3e4cc by Michael R. Crusoe at 2019-02-18T08:45:32Z
Remove trailing whitespace in debian/changelog
- - - - -
359c17b9 by Michael R. Crusoe at 2019-02-18T08:45:32Z
Remove trailing whitespace in debian/control
- - - - -
b10f26fe by Michael R. Crusoe at 2019-02-18T08:45:32Z
Remove trailing whitespace in debian/copyright
- - - - -
4 changed files:
- debian/changelog
- debian/control
- debian/copyright
- debian/rules
Changes:
=
debian/changelog
=
@@ -1,7 +1,18 @@
mira (4.9.6-5) UNRELEASED; urgency=medium
+ [ Andreas Tille ]
* Remove unneeded get-orig-source target
+ [ Michael R. Crusoe ]
+ * Update homepage URL
+ * Mark mira-doc as Multi-Arch: foreign
+ * Secure URI in copyright format
+ * Standards-Version: 4.3.0; no changes needed
+ * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
+ * Remove trailing whitespace in debian/changelog
+ * Remove trailing whitespace in debian/control
+ * Remove trailing whitespace in debian/copyright
+
-- Andreas Tille Wed, 19 Sep 2018 22:41:27 +0200
mira (4.9.6-4) unstable; urgency=medium
@@ -21,7 +32,7 @@ mira (4.9.6-4) unstable; urgency=medium
mira (4.9.6-3) unstable; urgency=medium
* Team upload.
-
+
[ Nadiya Sitdykova ]
* Add autopkgtest test-suite for denovo, mapping and est assembly
@@ -111,7 +122,7 @@ mira (4.0.2-1) unstable; urgency=low
mira (4.0-1) unstable; urgency=low
[ Thorsten Alteholz ]
- * New upstream version
+ * New upstream version
* debian/rules: add boost dir in auto_configure (Closes: #735798)
[ Andreas Tille ]
@@ -151,7 +162,7 @@ mira (3.9.17-1) unstable; urgency=low
* Add boost-minimal patch, to add boost-libraries in final linking,
fixing FTBFS (Closes: #701322)
* Enable parallel builds, to speed up compilation.
-
+
[ Andreas Tille ]
* delete debian/README.source which is outdated / wrong
* debian/*.1: Wrote / reviewed manpages for all installed programs
=
debian/control
=
@@ -25,10 +25,10 @@ Build-Depends: debhelper (>= 11~),
libboost-iostreams-dev
Build-Depends-Indep: docbook-xsl,
dblatex
-Standards-Version: 4.2.1
+Standards-Version: 4.3.0
Vcs-Browser: https://salsa.debian.org/med-team/mira
Vcs-Git: https://salsa.debian.org/med-team/mira.git
-Homepage: http://chevreux.org/projects_mira.html
+Homepage: https://sourceforge.net/p/mira-assembler/wiki/Home/
Package: mira-assembler
Architecture: any
@@ -51,7 +51,7 @@ Description: Whole Genome Shotgun and EST Sequence Assembler
sources for oligo design in clinical microarray experiments.
.
The package provides the following executables:
- Binaries provided:
+ Binaries provided:
* mira: for assembly of genome sequences
* miramem: estimating memory needed to assemble projects.
* mirabait: a "grep" like tool to select reads with kmers up to 256 bases.
@@ -73,6 +73,7 @@ Description: extract of RFAM 12 rRNA database
Package: mira-doc
Architecture: all
+Multi-Arch: foreign
Section: doc
Depends: ${misc:Depends}
Suggests: mira-assembler
=
debian/copyright
=
@@ -1,4 +1,4 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Contact: Bastien Chevreux
Source:
http://jaist.dl.sourceforge.net/project/mira-assembler/MIRA/V3rc2/mira-3rc2.tar.bz2
@@ -6,7 +6,7 @@ Files: *
Copyright: © 1997-2000 for MIRA V1.x and EdIt: Bastien Chevreux, Thomas
Pfisterer, Deutsches Krebsforschungszentrum Heidelberg -- Dept. of Molecula
Biophysics.
© 2001-2013 for MIRA V2.x: Bastien Chevreux
License: GPL-2+
-Comment:
+Comment:
Author of MIRA
.
Bastien Chevreux, formerly at the German Cancer Research Center (Deutsches
=
debian/rules
=
@@ -23,9 +23,14 @@ override_dh_auto_install-indep:
doc/docbook/doccss doc/docbook/DefinitiveGuideToMIRA.html || true
override_dh_auto_test-arch:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
make check
+endif
override_dh_auto_test-indep:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
+ echo no tests for -indep
+endif
override_dh_auto_build-arch:
# some *.cc files are c
[med-svn] [Git][med-team/mypy] Pushed new tag debian/0.670-1
Michael R. Crusoe pushed new tag debian/0.670-1 at Debian Med / mypy -- View it on GitLab: https://salsa.debian.org/med-team/mypy/tree/debian/0.670-1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/mypy][master] 6 commits: New upstream version 0.670
Michael R. Crusoe pushed to branch master at Debian Med / mypy Commits: 92291d5d by Michael R. Crusoe at 2019-02-09T07:06:29Z New upstream version 0.670 - - - - - b1869f67 by Michael R. Crusoe at 2019-02-09T07:06:40Z Update upstream source from tag upstream/0.670 Update to upstream version 0.670 with Debian dir f58d0b62d573331ceeaaf3938442566ae2951c07 - - - - - 5d00a890 by Michael R. Crusoe at 2019-02-09T07:08:50Z New upstream version - - - - - b3b9690c by Michael R. Crusoe at 2019-02-10T08:18:24Z bump and tighten the python3-typed-ast dependency - - - - - 002cc5e1 by Michael R. Crusoe at 2019-02-10T08:19:00Z more directories to clean - - - - - 340237ed by Michael R. Crusoe at 2019-02-10T08:19:22Z release to unstable - - - - - 30 changed files: - MANIFEST.in - PKG-INFO - debian/changelog - debian/clean - debian/control - docs/source/command_line.rst - docs/source/config_file.rst - docs/source/extending_mypy.rst - docs/source/getting_started.rst - docs/source/index.rst - docs/source/running_mypy.rst - + docs/source/stubgen.rst - mypy.egg-info/PKG-INFO - mypy.egg-info/SOURCES.txt - mypy.egg-info/requires.txt - mypy/api.py - mypy/build.py - mypy/checker.py - mypy/checkexpr.py - mypy/checkmember.py - mypy/checkstrformat.py - mypy/defaults.py - mypy/dmypy.py - mypy/dmypy_server.py - mypy/fastparse.py - mypy/fastparse2.py - mypy/fscache.py - mypy/interpreted_plugin.py - mypy/ipc.py - mypy/main.py The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/mypy/compare/00878f9d5037e39c6fec0a4954622249c3018a72...340237ed5c94a90f1318355c96b766f2f13ad2ed -- View it on GitLab: https://salsa.debian.org/med-team/mypy/compare/00878f9d5037e39c6fec0a4954622249c3018a72...340237ed5c94a90f1318355c96b766f2f13ad2ed You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/bcbio][master] bcbio-doc: mark as "Multi-Arch: foreign"
Michael R. Crusoe pushed to branch master at Debian Med / bcbio
Commits:
5e2407d6 by Michael R. Crusoe at 2019-02-10T08:36:48Z
bcbio-doc: mark as Multi-Arch: foreign
- - - - -
2 changed files:
- debian/changelog
- debian/control
Changes:
=
debian/changelog
=
@@ -1,3 +1,10 @@
+bcbio (1.1.2-4) UNRELEASED; urgency=medium
+
+ * Team upload.
+ * bcbio-doc: mark as "Multi-Arch: foreign"
+
+ -- Michael R. Crusoe Sun, 10 Feb 2019 00:35:08
-0800
+
bcbio (1.1.2-3) unstable; urgency=medium
* Demoted python3-seqcluster to become a recommendation
=
debian/control
=
@@ -71,6 +71,7 @@ Package: bcbio-doc
Architecture: all
Depends: ${sphinxdoc:Depends},${misc:Depends},
Suggests: bcbio|python3-bcbio
+Multi-Arch: foreign
Description: Documentation for RNAseq-workflows of bcbio(-nextgen)
This package provides the documentation for all aspects of the
workflows and technology of the bcbio-nextgen toolkit.
View it on GitLab:
https://salsa.debian.org/med-team/bcbio/commit/5e2407d63b681f9fa7949220147f279132213c62
--
View it on GitLab:
https://salsa.debian.org/med-team/bcbio/commit/5e2407d63b681f9fa7949220147f279132213c62
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[med-svn] [Git][med-team/mypy][master] Include upstream's README.md in the the mypy binary package.
Michael R. Crusoe pushed to branch master at Debian Med / mypy Commits: fb119329 by Michael R. Crusoe at 2019-02-10T08:25:07Z Include upstreams README.md in the the mypy binary package. - - - - - 2 changed files: - debian/changelog - + debian/mypy.docs Changes: = debian/changelog = @@ -1,3 +1,9 @@ +mypy (0.670-2) UNRELEASED; urgency=medium + + * Include upstream's README.md in the the mypy binary package. + + -- Michael R. Crusoe Sun, 10 Feb 2019 00:25:00 -0800 + mypy (0.670-1) unstable; urgency=medium * New upstream version = debian/mypy.docs = @@ -0,0 +1 @@ +README.md View it on GitLab: https://salsa.debian.org/med-team/mypy/commit/fb119329fe41090b56b672033433d4c0b6c64609 -- View it on GitLab: https://salsa.debian.org/med-team/mypy/commit/fb119329fe41090b56b672033433d4c0b6c64609 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/varna][master] 2 commits: update my email address
Michael R. Crusoe pushed to branch master at Debian Med / varna Commits: f3c46782 by Michael R. Crusoe at 2019-02-14T17:17:12Z update my email address - - - - - 1944e26f by Michael R. Crusoe at 2019-02-14T17:21:35Z Secure URI in copyright format; Standards-Version: 4.3.0 - - - - - 3 changed files: - debian/changelog - debian/control - debian/copyright Changes: = debian/changelog = @@ -1,3 +1,11 @@ +varna (3-93+ds-3) UNRELEASED; urgency=medium + + * Update my email address. + * Secure URI in copyright format + * Standards-Version: 4.3.0; no changes needed + + -- Michael R. Crusoe Thu, 14 Feb 2019 09:16:56 -0800 + varna (3-93+ds-2) unstable; urgency=medium * Team upload. = debian/control = @@ -1,12 +1,12 @@ Source: varna Maintainer: Debian Med Packaging Team -Uploaders: Michael R. Crusoe +Uploaders: Michael R. Crusoe Section: science Priority: optional Build-Depends: debhelper (>= 11~), javahelper, default-jdk -Standards-Version: 4.1.4 +Standards-Version: 4.3.0 Vcs-Browser: https://salsa.debian.org/med-team/varna Vcs-Git: https://salsa.debian.org/med-team/varna.git Homepage: http://varna.lri.fr/ = debian/copyright = @@ -1,4 +1,4 @@ -Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: VARNA Source: http://varna.lri.fr/index.php?lang=en=home=varna Files-Excluded: */*.class View it on GitLab: https://salsa.debian.org/med-team/varna/compare/fc299ed8d9107689c87b94d644b308a9bc6972f1...1944e26f2925a2f9d233499a73a731d118e3173c -- View it on GitLab: https://salsa.debian.org/med-team/varna/compare/fc299ed8d9107689c87b94d644b308a9bc6972f1...1944e26f2925a2f9d233499a73a731d118e3173c You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/python-gffutils][master] debhelper 11
Michael R. Crusoe pushed to branch master at Debian Med / python-gffutils Commits: 8de2e999 by Michael R. Crusoe at 2019-02-14T18:12:54Z debhelper 11 - - - - - 3 changed files: - debian/changelog - debian/compat - debian/control Changes: = debian/changelog = @@ -1,3 +1,9 @@ +python-gffutils (0.9-2) UNRELEASED; urgency=medium + + * debhelper 11 + + -- Michael R. Crusoe Thu, 14 Feb 2019 10:12:54 -0800 + python-gffutils (0.9-1) unstable; urgency=medium * Reupload after removal (#894298) = debian/compat = @@ -1 +1 @@ -10 +11 = debian/control = @@ -4,7 +4,7 @@ Uploaders: Michael R. Crusoe , Steffen Moeller Section: science Priority: optional -Build-Depends: debhelper (>= 10), +Build-Depends: debhelper (>= 11~), dh-python, bedtools, python3-all, View it on GitLab: https://salsa.debian.org/med-team/python-gffutils/commit/8de2e99908043d5d7a054c903cbb9f79eeb8e728 -- View it on GitLab: https://salsa.debian.org/med-team/python-gffutils/commit/8de2e99908043d5d7a054c903cbb9f79eeb8e728 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/bcbio] Pushed new tag debian/1.1.2-3
Michael R. Crusoe pushed new tag debian/1.1.2-3 at Debian Med / bcbio -- View it on GitLab: https://salsa.debian.org/med-team/bcbio/tree/debian/1.1.2-3 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/bcbio][master] 9 commits: New upstream version 1.1.3
Michael R. Crusoe pushed to branch master at Debian Med / bcbio
Commits:
d9e2b213 by Michael R. Crusoe at 2019-02-10T08:40:50Z
New upstream version 1.1.3
- - - - -
d4433341 by Michael R. Crusoe at 2019-02-10T08:41:40Z
Update upstream source from tag upstream/1.1.3
Update to upstream version 1.1.3
with Debian dir 66b4b7739104633ad67c5c4511f4d60bbbd50333
- - - - -
8d2a4655 by Michael R. Crusoe at 2019-02-10T08:42:51Z
new upstream release
- - - - -
5d78e887 by Michael R. Crusoe at 2019-02-10T08:45:24Z
debian/patches/python3.patch: removed, applied upstream
- - - - -
b2ff8b83 by Michael R. Crusoe at 2019-02-10T08:55:30Z
add ${sphinxdoc:Built-Using} to -doc
- - - - -
0b8fbcfe by Michael R. Crusoe at 2019-02-10T09:07:58Z
fixes a few spelling errors
- - - - -
63353604 by Michael R. Crusoe at 2019-02-10T09:07:58Z
add pytest to enable running the tests
- - - - -
f188722a by Michael R. Crusoe at 2019-02-10T09:07:59Z
python3-bcbio: section is python
- - - - -
7b98f981 by Michael R. Crusoe at 2019-02-11T07:13:40Z
Add recommendations discovered through testing
and make a list of software that needs packaging
- - - - -
30 changed files:
- .travis.yml
- HISTORY.md
- bcbio/bam/__init__.py
- bcbio/bam/callable.py
- bcbio/bam/cram.py
- bcbio/bam/fastq.py
- bcbio/broad/__init__.py
- bcbio/cwl/create.py
- bcbio/cwl/cwlutils.py
- bcbio/cwl/defs.py
- bcbio/cwl/hpc.py
- bcbio/cwl/tool.py
- bcbio/cwl/workflow.py
- bcbio/distributed/multi.py
- bcbio/distributed/objectstore.py
- bcbio/distributed/resources.py
- bcbio/distributed/runfn.py
- bcbio/distributed/split.py
- bcbio/galaxy/api.py
- bcbio/galaxy/nglims.py
- bcbio/graph/graph.py
- bcbio/heterogeneity/bubbletree.py
- bcbio/heterogeneity/chromhacks.py
- bcbio/heterogeneity/loh.py
- bcbio/hla/bwakit.py
- bcbio/illumina/flowcell.py
- bcbio/illumina/machine.py
- bcbio/illumina/samplesheet.py
- bcbio/illumina/transfer.py
- bcbio/install.py
The diff was not included because it is too large.
View it on GitLab:
https://salsa.debian.org/med-team/bcbio/compare/5e2407d63b681f9fa7949220147f279132213c62...7b98f981e77e80d109e7b14e4cacc2e544a480a1
--
View it on GitLab:
https://salsa.debian.org/med-team/bcbio/compare/5e2407d63b681f9fa7949220147f279132213c62...7b98f981e77e80d109e7b14e4cacc2e544a480a1
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[med-svn] [Git][med-team/bcbio][pristine-tar] pristine-tar data for bcbio_1.1.3.orig.tar.gz
Michael R. Crusoe pushed to branch pristine-tar at Debian Med / bcbio Commits: cbdf0d82 by Michael R. Crusoe at 2019-02-10T08:41:40Z pristine-tar data for bcbio_1.1.3.orig.tar.gz - - - - - 2 changed files: - + bcbio_1.1.3.orig.tar.gz.delta - + bcbio_1.1.3.orig.tar.gz.id Changes: = bcbio_1.1.3.orig.tar.gz.delta = Binary files /dev/null and b/bcbio_1.1.3.orig.tar.gz.delta differ = bcbio_1.1.3.orig.tar.gz.id = @@ -0,0 +1 @@ +763af61f5c3ea631d1b78fc2c3e1f9ad6b148ebd View it on GitLab: https://salsa.debian.org/med-team/bcbio/commit/cbdf0d8249438a3b9eec06d1bc3bff29e5eca530 -- View it on GitLab: https://salsa.debian.org/med-team/bcbio/commit/cbdf0d8249438a3b9eec06d1bc3bff29e5eca530 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/bcbio] Pushed new tag upstream/1.1.3
Michael R. Crusoe pushed new tag upstream/1.1.3 at Debian Med / bcbio -- View it on GitLab: https://salsa.debian.org/med-team/bcbio/tree/upstream/1.1.3 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/bcbio][upstream] New upstream version 1.1.3
Michael R. Crusoe pushed to branch upstream at Debian Med / bcbio Commits: d9e2b213 by Michael R. Crusoe at 2019-02-10T08:40:50Z New upstream version 1.1.3 - - - - - 30 changed files: - .travis.yml - HISTORY.md - bcbio/bam/__init__.py - bcbio/bam/callable.py - bcbio/bam/cram.py - bcbio/bam/fastq.py - bcbio/broad/__init__.py - bcbio/cwl/create.py - bcbio/cwl/cwlutils.py - bcbio/cwl/defs.py - bcbio/cwl/hpc.py - bcbio/cwl/tool.py - bcbio/cwl/workflow.py - bcbio/distributed/multi.py - bcbio/distributed/objectstore.py - bcbio/distributed/resources.py - bcbio/distributed/runfn.py - bcbio/distributed/split.py - bcbio/galaxy/api.py - bcbio/galaxy/nglims.py - bcbio/graph/graph.py - bcbio/heterogeneity/bubbletree.py - bcbio/heterogeneity/chromhacks.py - bcbio/heterogeneity/loh.py - bcbio/hla/bwakit.py - bcbio/illumina/flowcell.py - bcbio/illumina/machine.py - bcbio/illumina/samplesheet.py - bcbio/illumina/transfer.py - bcbio/install.py The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/bcbio/commit/d9e2b213d053cd3071fde18f521f7130cd609da0 -- View it on GitLab: https://salsa.debian.org/med-team/bcbio/commit/d9e2b213d053cd3071fde18f521f7130cd609da0 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libthread-pool][master] 3 commits: document Standards-Version: 4.3.0; no changes needed
Michael R. Crusoe pushed to branch master at Debian Med / libthread-pool
Commits:
666efa01 by Michael R. Crusoe at 2019-02-15T15:52:00Z
document Standards-Version: 4.3.0; no changes needed
- - - - -
f8ff75e9 by Michael R. Crusoe at 2019-02-15T15:55:24Z
Update homepage URL.
- - - - -
2002dac2 by Michael R. Crusoe at 2019-02-15T16:38:35Z
build run the tests
- - - - -
6 changed files:
- debian/changelog
- debian/control
- debian/rules
- + debian/tests/CMakeLists.txt
- + debian/tests/control
- + debian/tests/run-unit-test
Changes:
=
debian/changelog
=
@@ -3,6 +3,11 @@ libthread-pool (1.0.0-3) UNRELEASED; urgency=medium
* Team upload.
* Add missing '-pthread'
* Remove trailing whitespace in debian/copyright
+ * Standards-Version: 4.3.0; no changes needed
+ * Update homepage URL.
+ * Build the included tests and run them
+ * As an autopkgtest, build the tests against the installed package and run
+them.
-- Michael R. Crusoe Fri, 04 Jan 2019 09:44:11
-0800
=
debian/control
=
@@ -7,11 +7,11 @@ Build-Depends: debhelper (>= 11~),
cmake,
d-shlibs,
rename,
- libgtest-dev
+ googletest
Standards-Version: 4.3.0
Vcs-Browser: https://salsa.debian.org/med-team/libthread-pool
Vcs-Git: https://salsa.debian.org/med-team/libthread-pool.git
-Homepage: https://github.com/rvaser/libthread-pool
+Homepage: https://github.com/rvaser/thread_pool
Package: libthread-pool0
Architecture: any
=
debian/rules
=
@@ -8,6 +8,14 @@ export DEB_LDFLAGS_MAINT_APPEND+=-pthread
%:
dh $@
+override_dh_auto_configure:
+ rm -Rf vendor/*
+ ln -s /usr/src/googletest ./vendor/
+ dh_auto_configure -- -Dthread_pool_build_tests=ON
+
+override_dh_auto_test:
+ ./obj-*/bin/thread_pool_test
+
override_dh_install:
dh_install
file-rename 's/_static\.a/.a/' `find debian -name "lib*_static.a"`
=
debian/tests/CMakeLists.txt
=
@@ -0,0 +1,10 @@
+cmake_minimum_required(VERSION 3.2)
+project(thread_pool_test)
+
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra -pedantic")
+set(CMAKE_CXX_STANDARD 11)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+
+add_executable(thread_pool_test thread_pool_test.cpp)
+add_subdirectory(/usr/src/googletest .. EXCLUDE_FROM_ALL)
+target_link_libraries(thread_pool_test thread_pool gtest_main)
=
debian/tests/control
=
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @, googletest
+Restrictions: allow-stderr
=
debian/tests/run-unit-test
=
@@ -0,0 +1,19 @@
+#!/bin/bash
+set -e
+
+pkg=libthread-pool
+
+if [ "$AUTOPKGTEST_TMP" = "" ] ; then
+ AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XX`
+ trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp -a test/* $AUTOPKGTEST_TMP
+cp -a debian/tests/CMakeLists.txt $AUTOPKGTEST_TMP
+
+cd $AUTOPKGTEST_TMP
+mkdir build
+cd build
+cmake ..
+make
+./thread_pool_test
View it on GitLab:
https://salsa.debian.org/med-team/libthread-pool/compare/3c7859620f1255bf119d6acf036e0a13a2382570...2002dac22bc3da565f4a5820664986a5d44a62e8
--
View it on GitLab:
https://salsa.debian.org/med-team/libthread-pool/compare/3c7859620f1255bf119d6acf036e0a13a2382570...2002dac22bc3da565f4a5820664986a5d44a62e8
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[med-svn] [Git][med-team/hhsuite][master] Don't build with -march=native
Michael R. Crusoe pushed to branch master at Debian Med / hhsuite
Commits:
d46775c0 by Michael R. Crusoe at 2019-02-15T15:08:46Z
Dont build with -march=native
- - - - -
2 changed files:
- debian/changelog
- debian/patches/disable-AVX-SSE.patch
Changes:
=
debian/changelog
=
@@ -1,7 +1,13 @@
-hhsuite (3.0~beta3+dfsg-3) UNRELEASED; urgency=medium
+hhsuite (3.0~beta3+dfsg-3) UNRELEASED; urgency=high
+ * Team upload
+
+ [ Andreas Tille ]
* Build against ffindex (>= 0.9.9.8)
+ [ Michael R. Crusoe ]
+ * Don't build iwht -march=native
+
-- Andreas Tille Fri, 11 Jan 2019 13:05:23 +0100
hhsuite (3.0~beta3+dfsg-2) unstable; urgency=medium
=
debian/patches/disable-AVX-SSE.patch
=
@@ -1,10 +1,8 @@
Description: do not use AVX to build binaries
Author: Sascha Steinbiss
-Index: hhsuite/src/CMakeLists.txt
-===
--- hhsuite.orig/src/CMakeLists.txt
+++ hhsuite/src/CMakeLists.txt
-@@ -12,22 +12,22 @@ endif()
+@@ -12,22 +12,22 @@
if(X86 OR X86_64)
#SSE
@@ -35,11 +33,24 @@ Index: hhsuite/src/CMakeLists.txt
endif()
else() #
-Index: hhsuite/cmake/CheckSSEFeatures.cmake
-===
--- hhsuite.orig/cmake/CheckSSEFeatures.cmake
+++ hhsuite/cmake/CheckSSEFeatures.cmake
-@@ -209,23 +209,23 @@ macro(PCL_CHECK_FOR_SSE)
+@@ -14,10 +14,10 @@
+ if(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX)
+ execute_process(COMMAND ${CMAKE_CXX_COMPILER} "-dumpversion"
+ OUTPUT_VARIABLE GCC_VERSION_STRING)
+-if(GCC_VERSION_STRING VERSION_GREATER 4.2 AND NOT APPLE AND NOT
CMAKE_CROSSCOMPILING)
+-SET(SSE_FLAGS "${SSE_FLAGS} -march=native")
+-message(STATUS "Using CPU native flags for SSE optimization:
${SSE_FLAGS}")
+-endif()
++ # if(GCC_VERSION_STRING VERSION_GREATER 4.2 AND NOT APPLE AND NOT
CMAKE_CROSSCOMPILING)
++# SET(SSE_FLAGS "${SSE_FLAGS} -march=native")
++# message(STATUS "Using CPU native flags for SSE optimization:
${SSE_FLAGS}")
++# endif()
+ endif()
+
+ # Unfortunately we need to check for SSE to enable "-mfpmath=sse"
alongside
+@@ -209,23 +209,23 @@
set(CMAKE_REQUIRED_FLAGS)
if(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX OR
CMAKE_COMPILER_IS_CLANG)
View it on GitLab:
https://salsa.debian.org/med-team/hhsuite/commit/d46775c038b7fecc432b5d38886ad590353d9418
--
View it on GitLab:
https://salsa.debian.org/med-team/hhsuite/commit/d46775c038b7fecc432b5d38886ad590353d9418
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[med-svn] [Git][med-team/t-coffee][master] 2 commits: Don't hide the build flags
Michael R. Crusoe pushed to branch master at Debian Med / t-coffee
Commits:
a7229134 by Michael R. Crusoe at 2019-02-15T14:51:38Z
Dont hide the build flags
- - - - -
48d6ff02 by Michael R. Crusoe at 2019-02-15T14:52:52Z
t-coffee-examples: mark Multi-Arch: foreign
- - - - -
4 changed files:
- debian/changelog
- debian/control
- debian/patches/series
- + debian/patches/verbose_build
Changes:
=
debian/changelog
=
@@ -1,3 +1,11 @@
+t-coffee (12.00.7fb08c2-5) UNRELEASED; urgency=medium
+
+ * Team upload.
+ * Unhide the build flags.
+ * t-coffee-examples: mark Multi-Arch: foreign
+
+ -- Michael R. Crusoe Fri, 15 Feb 2019 06:49:18
-0800
+
t-coffee (12.00.7fb08c2-4) unstable; urgency=medium
[ Helmut Grohne ]
=
debian/control
=
@@ -55,6 +55,7 @@ Description: Multiple Sequence Alignment
Package: t-coffee-examples
Architecture: all
+Multi-Arch: foreign
Depends: ${misc:Depends}
Recommends: t-coffee
Description: annotated examples for the use of T-Coffee
=
debian/patches/series
=
@@ -7,3 +7,4 @@ mayhem.patch
stable-linking-inputs.patch
clustalw2.patch
fix_tempfile_name_sharing.patch
+verbose_build
=
debian/patches/verbose_build
=
@@ -0,0 +1,19 @@
+Author: Michael R. Crusoe
+Description: don't hide the build flags
+--- t-coffee.orig/t_coffee_source/makefile
t-coffee/t_coffee_source/makefile
+@@ -5,10 +5,12 @@
+ DEPS := $(OBJECTS:.o=.deps)
+
+ t_coffee: $(OBJECTS)
+- @echo " Linking..."; $(CC) $^ -o t_coffee -lm $(LDFLAGS)
++ @echo " Linking..."
++ $(CC) $^ -o t_coffee -lm $(LDFLAGS)
+
+ %.o: %.c
+- @echo " CC $<"; $(CC) $(CPPFLAGS) $(CFLAGS) -I. -MD -MF $(@:.o=.deps)
-c -o $@ $<
++ @echo " CC $<"
++ $(CC) $(CPPFLAGS) $(CFLAGS) -I. -MD -MF $(@:.o=.deps) -c -o $@ $<
+
+ -include $(DEPS)
+
View it on GitLab:
https://salsa.debian.org/med-team/t-coffee/compare/de16e40e73bd619332e2114d8dd702b7088e...48d6ff022c3bf00cc14f3cb1fbf81946ed4caabc
--
View it on GitLab:
https://salsa.debian.org/med-team/t-coffee/compare/de16e40e73bd619332e2114d8dd702b7088e...48d6ff022c3bf00cc14f3cb1fbf81946ed4caabc
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[med-svn] [Git][med-team/abyss] Pushed new tag debian/2.1.5-5
Michael R. Crusoe pushed new tag debian/2.1.5-5 at Debian Med / abyss -- View it on GitLab: https://salsa.debian.org/med-team/abyss/tree/debian/2.1.5-5 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/abyss][master] release to unstable
Michael R. Crusoe pushed to branch master at Debian Med / abyss Commits: 6f1b2f2f by Michael R. Crusoe at 2019-02-15T14:24:02Z release to unstable - - - - - 1 changed file: - debian/changelog Changes: = debian/changelog = @@ -1,9 +1,9 @@ -abyss (2.1.5-5) UNRELEASED; urgency=medium +abyss (2.1.5-5) unstable; urgency=medium * Team upload. * Fix MPI build. Closes: #922351 - -- Michael R. Crusoe Fri, 15 Feb 2019 05:37:20 -0800 + -- Michael R. Crusoe Fri, 15 Feb 2019 06:23:47 -0800 abyss (2.1.5-4) unstable; urgency=medium View it on GitLab: https://salsa.debian.org/med-team/abyss/commit/6f1b2f2fc6005b4d579db07eac55981d16a26720 -- View it on GitLab: https://salsa.debian.org/med-team/abyss/commit/6f1b2f2fc6005b4d579db07eac55981d16a26720 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/abyss][master] Fix MPI build
Michael R. Crusoe pushed to branch master at Debian Med / abyss Commits: 0149298f by Michael R. Crusoe at 2019-02-15T14:23:32Z Fix MPI build - - - - - 4 changed files: - debian/changelog - debian/control - debian/rules - debian/tests/run-unit-test Changes: = debian/changelog = @@ -1,3 +1,10 @@ +abyss (2.1.5-5) UNRELEASED; urgency=medium + + * Team upload. + * Fix MPI build. Closes: #922351 + + -- Michael R. Crusoe Fri, 15 Feb 2019 05:37:20 -0800 + abyss (2.1.5-4) unstable; urgency=medium * Fix build on hurd due to missing header file (thanks for the patch = debian/control = @@ -10,7 +10,8 @@ Build-Depends: debhelper (>= 12~), libsparsehash-dev, libtext-multimarkdown-perl, libgtest-dev, - libsqlite3-dev + libsqlite3-dev, + pkg-config Standards-Version: 4.3.0 Vcs-Browser: https://salsa.debian.org/med-team/abyss Vcs-Git: https://salsa.debian.org/med-team/abyss.git = debian/rules = @@ -10,7 +10,8 @@ export DH_OPTIONS dh $@ override_dh_auto_configure: - dh_auto_configure -- --with-mpi=/usr/lib/openmpi + dh_auto_configure -- \ + --with-mpi=$(shell pkg-config mpi --variable=includedir | sed s=/include==) override_dh_auto_build: dh_auto_build = debian/tests/run-unit-test = @@ -14,6 +14,8 @@ gunzip -r * abyss-pe k=25 name=test in='test-data/reads1.fastq test-data/reads2.fastq' +echo Testing mpi compilation +/usr/lib/abyss/ABYSS-P --help View it on GitLab: https://salsa.debian.org/med-team/abyss/commit/0149298fc0016196f025482f8f1f61cc8b0d0632 -- View it on GitLab: https://salsa.debian.org/med-team/abyss/commit/0149298fc0016196f025482f8f1f61cc8b0d0632 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libthread-pool][master] respect nocheck
Michael R. Crusoe pushed to branch master at Debian Med / libthread-pool Commits: aaea68ed by Michael R. Crusoe at 2019-02-15T16:43:47Z respect nocheck - - - - - 2 changed files: - debian/control - debian/rules Changes: = debian/control = @@ -7,7 +7,7 @@ Build-Depends: debhelper (>= 11~), cmake, d-shlibs, rename, - googletest + googletest Standards-Version: 4.3.0 Vcs-Browser: https://salsa.debian.org/med-team/libthread-pool Vcs-Git: https://salsa.debian.org/med-team/libthread-pool.git = debian/rules = @@ -14,7 +14,9 @@ override_dh_auto_configure: dh_auto_configure -- -Dthread_pool_build_tests=ON override_dh_auto_test: +ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS))) ./obj-*/bin/thread_pool_test +endif override_dh_install: dh_install View it on GitLab: https://salsa.debian.org/med-team/libthread-pool/commit/aaea68edb31ef65037ead8da0abe67638639a8bd -- View it on GitLab: https://salsa.debian.org/med-team/libthread-pool/commit/aaea68edb31ef65037ead8da0abe67638639a8bd You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
